PDB Short entry for 2XCV HEADER HYDROLASE 26-APR-10 2XCV TITLE CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II TITLE 2 IN COMPLEX WITH INOSINE MONOPHOSPHATE AND 2,3-BISPHOSPHOGLYCERATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSOLIC PURINE 5'-NUCLEOTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOSOLIC 5'-NUCLEOTIDASE II; COMPND 5 EC: 3.1.3.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3 PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: P28A-LIC KEYWDS HYDROLASE, METAL-BINDING, NUCLEOTIDE METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR K.WALLDEN,P.NORDLUND REVDAT 4 20-DEC-23 2XCV 1 REMARK LINK REVDAT 3 20-JUL-16 2XCV 1 REMARK HETNAM HETSYN MASTER REVDAT 2 27-APR-11 2XCV 1 SOURCE JRNL REMARK REVDAT 1 16-MAR-11 2XCV 0 JRNL AUTH K.WALLDEN,P.NORDLUND JRNL TITL STRUCTURAL BASIS FOR THE ALLOSTERIC REGULATION AND SUBSTRATE JRNL TITL 2 RECOGNITION OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II JRNL REF J.MOL.BIOL. V. 408 684 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21396942 JRNL DOI 10.1016/J.JMB.2011.02.059 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 32486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1729 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2364 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3767 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 258 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.16000 REMARK 3 B22 (A**2) : 1.08000 REMARK 3 B33 (A**2) : -2.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.212 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.192 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.283 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4025 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5452 ; 1.849 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 482 ; 6.592 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;33.158 ;22.812 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 699 ;16.823 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.439 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 570 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3081 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1717 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2742 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 252 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.063 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 54 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.168 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2436 ; 1.218 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3821 ; 2.021 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1830 ; 3.059 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1631 ; 4.410 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2XCV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0081 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : DYNAMICALLY BENDABLE REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34216 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2JCM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.78500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.89500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.30500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.78500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.89500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.30500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.78500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.89500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 65.30500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.78500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.89500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.30500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 74170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 130.61000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 130.61000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 52 TO ASN REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 VAL A -4 REMARK 465 PRO A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ILE A 397 REMARK 465 PHE A 398 REMARK 465 LEU A 399 REMARK 465 ALA A 400 REMARK 465 GLU A 401 REMARK 465 LEU A 402 REMARK 465 TYR A 403 REMARK 465 LYS A 404 REMARK 465 HIS A 405 REMARK 465 LEU A 406 REMARK 465 ASP A 407 REMARK 465 SER A 408 REMARK 465 SER A 409 REMARK 465 SER A 410 REMARK 465 ASN A 411 REMARK 465 GLU A 412 REMARK 465 ARG A 413 REMARK 465 PRO A 414 REMARK 465 ASP A 415 REMARK 465 ILE A 416 REMARK 465 SER A 417 REMARK 465 SER A 418 REMARK 465 ILE A 419 REMARK 465 GLN A 420 REMARK 465 THR A 489 REMARK 465 VAL A 490 REMARK 465 GLU A 491 REMARK 465 HIS A 492 REMARK 465 THR A 493 REMARK 465 HIS A 494 REMARK 465 VAL A 495 REMARK 465 ASP A 496 REMARK 465 ILE A 497 REMARK 465 ASN A 498 REMARK 465 GLU A 499 REMARK 465 MET A 500 REMARK 465 GLU A 501 REMARK 465 SER A 502 REMARK 465 PRO A 503 REMARK 465 LEU A 504 REMARK 465 ALA A 505 REMARK 465 THR A 506 REMARK 465 ARG A 507 REMARK 465 ASN A 508 REMARK 465 ARG A 509 REMARK 465 THR A 510 REMARK 465 SER A 511 REMARK 465 VAL A 512 REMARK 465 ASP A 513 REMARK 465 PHE A 514 REMARK 465 LYS A 515 REMARK 465 ASP A 516 REMARK 465 THR A 517 REMARK 465 ASP A 518 REMARK 465 TYR A 519 REMARK 465 LYS A 520 REMARK 465 ARG A 521 REMARK 465 HIS A 522 REMARK 465 GLN A 523 REMARK 465 LEU A 524 REMARK 465 THR A 525 REMARK 465 ARG A 526 REMARK 465 SER A 527 REMARK 465 ILE A 528 REMARK 465 SER A 529 REMARK 465 GLU A 530 REMARK 465 ILE A 531 REMARK 465 LYS A 532 REMARK 465 PRO A 533 REMARK 465 PRO A 534 REMARK 465 ASN A 535 REMARK 465 LEU A 536 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 48 CB CYS A 48 SG -0.124 REMARK 500 TYR A 60 CZ TYR A 60 CE2 0.084 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 277 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 277 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 MET A 53 -69.30 -98.54 REMARK 500 THR A 56 -73.90 -121.20 REMARK 500 PRO A 267 36.77 -83.28 REMARK 500 PHE A 354 -66.28 -93.39 REMARK 500 ILE A 357 -63.91 -92.80 REMARK 500 ASP A 384 40.27 -81.63 REMARK 500 LYS A 385 30.69 -153.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2013 DISTANCE = 5.82 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1492 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 52 ND2 REMARK 620 2 ASP A 54 O 90.3 REMARK 620 3 ASP A 351 OD1 81.9 82.9 REMARK 620 4 IMP A1491 O2P 96.4 105.5 171.5 REMARK 620 5 HOH A2215 O 172.6 87.2 90.9 91.0 REMARK 620 6 HOH A2218 O 84.0 167.9 85.7 85.8 97.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DG2 A 1489 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1490 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMP A 1491 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1492 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JC9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX REMARK 900 WITH ADENOSINE REMARK 900 RELATED ID: 2XJD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH INORGANIC PHOSPHATE AND DEOXYADENOSINE REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 2XJF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE REMARK 900 II WITH A COVALENTLY MODIFIED ASN52 REMARK 900 RELATED ID: 2J2C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II (NT5C2, CN- REMARK 900 II) REMARK 900 RELATED ID: 2JCM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX REMARK 900 WITH BERYLLIUM TRIFLUORIDE REMARK 900 RELATED ID: 2XCX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APOFORM OF THE D52N VARIANT OF CYTOSOLIC 5' REMARK 900 -NUCLEOTIDASE II REMARK 900 RELATED ID: 2XJE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH URIDINE 5'- MONOPHOSPHATE AND ADENOSINE REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 2XCW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND ATP REMARK 900 RELATED ID: 2XJB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH DEOXYGUANOSINE MONOPHOSPHATE AND DEOXYADENOSINE REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 2XJC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH GUANOSINE MONOPHOSPHATE AND DIADENOSINE REMARK 900 TETRAPHOSPHATE DBREF 2XCV A 1 536 UNP P49902 5NTC_HUMAN 1 536 SEQADV 2XCV GLY A -17 UNP P49902 EXPRESSION TAG SEQADV 2XCV SER A -16 UNP P49902 EXPRESSION TAG SEQADV 2XCV SER A -15 UNP P49902 EXPRESSION TAG SEQADV 2XCV HIS A -14 UNP P49902 EXPRESSION TAG SEQADV 2XCV HIS A -13 UNP P49902 EXPRESSION TAG SEQADV 2XCV HIS A -12 UNP P49902 EXPRESSION TAG SEQADV 2XCV HIS A -11 UNP P49902 EXPRESSION TAG SEQADV 2XCV HIS A -10 UNP P49902 EXPRESSION TAG SEQADV 2XCV HIS A -9 UNP P49902 EXPRESSION TAG SEQADV 2XCV SER A -8 UNP P49902 EXPRESSION TAG SEQADV 2XCV SER A -7 UNP P49902 EXPRESSION TAG SEQADV 2XCV GLY A -6 UNP P49902 EXPRESSION TAG SEQADV 2XCV LEU A -5 UNP P49902 EXPRESSION TAG SEQADV 2XCV VAL A -4 UNP P49902 EXPRESSION TAG SEQADV 2XCV PRO A -3 UNP P49902 EXPRESSION TAG SEQADV 2XCV ARG A -2 UNP P49902 EXPRESSION TAG SEQADV 2XCV GLY A -1 UNP P49902 EXPRESSION TAG SEQADV 2XCV SER A 0 UNP P49902 EXPRESSION TAG SEQADV 2XCV ASN A 52 UNP P49902 ASP 52 ENGINEERED MUTATION SEQRES 1 A 554 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 554 VAL PRO ARG GLY SER MET SER THR SER TRP SER ASP ARG SEQRES 3 A 554 LEU GLN ASN ALA ALA ASP MET PRO ALA ASN MET ASP LYS SEQRES 4 A 554 HIS ALA LEU LYS LYS TYR ARG ARG GLU ALA TYR HIS ARG SEQRES 5 A 554 VAL PHE VAL ASN ARG SER LEU ALA MET GLU LYS ILE LYS SEQRES 6 A 554 CYS PHE GLY PHE ASN MET ASP TYR THR LEU ALA VAL TYR SEQRES 7 A 554 LYS SER PRO GLU TYR GLU SER LEU GLY PHE GLU LEU THR SEQRES 8 A 554 VAL GLU ARG LEU VAL SER ILE GLY TYR PRO GLN GLU LEU SEQRES 9 A 554 LEU SER PHE ALA TYR ASP SER THR PHE PRO THR ARG GLY SEQRES 10 A 554 LEU VAL PHE ASP THR LEU TYR GLY ASN LEU LEU LYS VAL SEQRES 11 A 554 ASP ALA TYR GLY ASN LEU LEU VAL CYS ALA HIS GLY PHE SEQRES 12 A 554 ASN PHE ILE ARG GLY PRO GLU THR ARG GLU GLN TYR PRO SEQRES 13 A 554 ASN LYS PHE ILE GLN ARG ASP ASP THR GLU ARG PHE TYR SEQRES 14 A 554 ILE LEU ASN THR LEU PHE ASN LEU PRO GLU THR TYR LEU SEQRES 15 A 554 LEU ALA CYS LEU VAL ASP PHE PHE THR ASN CYS PRO ARG SEQRES 16 A 554 TYR THR SER CYS GLU THR GLY PHE LYS ASP GLY ASP LEU SEQRES 17 A 554 PHE MET SER TYR ARG SER MET PHE GLN ASP VAL ARG ASP SEQRES 18 A 554 ALA VAL ASP TRP VAL HIS TYR LYS GLY SER LEU LYS GLU SEQRES 19 A 554 LYS THR VAL GLU ASN LEU GLU LYS TYR VAL VAL LYS ASP SEQRES 20 A 554 GLY LYS LEU PRO LEU LEU LEU SER ARG MET LYS GLU VAL SEQRES 21 A 554 GLY LYS VAL PHE LEU ALA THR ASN SER ASP TYR LYS TYR SEQRES 22 A 554 THR ASP LYS ILE MET THR TYR LEU PHE ASP PHE PRO HIS SEQRES 23 A 554 GLY PRO LYS PRO GLY SER SER HIS ARG PRO TRP GLN SER SEQRES 24 A 554 TYR PHE ASP LEU ILE LEU VAL ASP ALA ARG LYS PRO LEU SEQRES 25 A 554 PHE PHE GLY GLU GLY THR VAL LEU ARG GLN VAL ASP THR SEQRES 26 A 554 LYS THR GLY LYS LEU LYS ILE GLY THR TYR THR GLY PRO SEQRES 27 A 554 LEU GLN HIS GLY ILE VAL TYR SER GLY GLY SER SER ASP SEQRES 28 A 554 THR ILE CYS ASP LEU LEU GLY ALA LYS GLY LYS ASP ILE SEQRES 29 A 554 LEU TYR ILE GLY ASP HIS ILE PHE GLY ASP ILE LEU LYS SEQRES 30 A 554 SER LYS LYS ARG GLN GLY TRP ARG THR PHE LEU VAL ILE SEQRES 31 A 554 PRO GLU LEU ALA GLN GLU LEU HIS VAL TRP THR ASP LYS SEQRES 32 A 554 SER SER LEU PHE GLU GLU LEU GLN SER LEU ASP ILE PHE SEQRES 33 A 554 LEU ALA GLU LEU TYR LYS HIS LEU ASP SER SER SER ASN SEQRES 34 A 554 GLU ARG PRO ASP ILE SER SER ILE GLN ARG ARG ILE LYS SEQRES 35 A 554 LYS VAL THR HIS ASP MET ASP MET CYS TYR GLY MET MET SEQRES 36 A 554 GLY SER LEU PHE ARG SER GLY SER ARG GLN THR LEU PHE SEQRES 37 A 554 ALA SER GLN VAL MET ARG TYR ALA ASP LEU TYR ALA ALA SEQRES 38 A 554 SER PHE ILE ASN LEU LEU TYR TYR PRO PHE SER TYR LEU SEQRES 39 A 554 PHE ARG ALA ALA HIS VAL LEU MET PRO HIS GLU SER THR SEQRES 40 A 554 VAL GLU HIS THR HIS VAL ASP ILE ASN GLU MET GLU SER SEQRES 41 A 554 PRO LEU ALA THR ARG ASN ARG THR SER VAL ASP PHE LYS SEQRES 42 A 554 ASP THR ASP TYR LYS ARG HIS GLN LEU THR ARG SER ILE SEQRES 43 A 554 SER GLU ILE LYS PRO PRO ASN LEU HET DG2 A1489 15 HET GOL A1490 6 HET IMP A1491 23 HET MG A1492 1 HETNAM DG2 (2R)-2,3-DIPHOSPHOGLYCERIC ACID HETNAM GOL GLYCEROL HETNAM IMP INOSINIC ACID HETNAM MG MAGNESIUM ION HETSYN DG2 2,3-BISPHOSPHOGLYCERIC ACID; 2,3-BISPHOSPHOGLYCERATE; HETSYN 2 DG2 2,3-BPG; 2,3-DIPHOSPHOGLYCERIC ACID; 2,3- HETSYN 3 DG2 DIPHOSPHOGLYCERATE; 2,3-DPG; (2~{R})-2,3- HETSYN 4 DG2 DIPHOSPHONOOXYPROPANOIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DG2 C3 H8 O10 P2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 IMP C10 H13 N4 O8 P FORMUL 5 MG MG 2+ FORMUL 6 HOH *258(H2 O) HELIX 1 1 SER A 4 MET A 15 1 12 HELIX 2 2 ASP A 20 ARG A 28 1 9 HELIX 3 3 ARG A 29 ARG A 34 5 6 HELIX 4 4 GLU A 44 ILE A 46 5 3 HELIX 5 5 PRO A 63 ILE A 80 1 18 HELIX 6 6 PRO A 83 PHE A 89 5 7 HELIX 7 7 ARG A 129 TYR A 137 1 9 HELIX 8 8 THR A 155 PHE A 157 5 3 HELIX 9 9 ASN A 158 CYS A 175 1 18 HELIX 10 10 TYR A 194 LYS A 211 1 18 HELIX 11 11 SER A 213 GLU A 220 1 8 HELIX 12 12 ASN A 221 VAL A 226 1 6 HELIX 13 13 LYS A 231 GLY A 243 1 13 HELIX 14 14 ASP A 252 PHE A 264 1 13 HELIX 15 15 PRO A 278 PHE A 283 5 6 HELIX 16 16 PRO A 293 GLY A 297 5 5 HELIX 17 17 SER A 331 LEU A 339 1 9 HELIX 18 18 LYS A 342 LYS A 344 5 3 HELIX 19 19 HIS A 352 ASP A 356 1 5 HELIX 20 20 ILE A 357 GLY A 365 1 9 HELIX 21 21 GLU A 374 ASP A 384 1 11 HELIX 22 22 LYS A 385 ASP A 396 1 12 HELIX 23 23 ARG A 421 CYS A 433 1 13 HELIX 24 24 THR A 448 ALA A 458 1 11 HELIX 25 25 SER A 464 TYR A 471 5 8 HELIX 26 26 MET A 484 SER A 488 5 5 SHEET 1 AA 9 PHE A 36 VAL A 37 0 SHEET 2 AA 9 LEU A 460 ALA A 462 -1 O TYR A 461 N PHE A 36 SHEET 3 AA 9 ARG A 367 VAL A 371 1 O THR A 368 N LEU A 460 SHEET 4 AA 9 ILE A 346 GLY A 350 1 O ILE A 346 N ARG A 367 SHEET 5 AA 9 CYS A 48 PHE A 51 1 O CYS A 48 N LEU A 347 SHEET 6 AA 9 LYS A 244 ALA A 248 1 O LYS A 244 N PHE A 49 SHEET 7 AA 9 LEU A 285 VAL A 288 1 O LEU A 285 N LEU A 247 SHEET 8 AA 9 VAL A 326 GLY A 329 1 O TYR A 327 N VAL A 288 SHEET 9 AA 9 LEU A 302 VAL A 305 -1 O ARG A 303 N SER A 328 SHEET 1 AB 2 LEU A 41 ALA A 42 0 SHEET 2 AB 2 LEU A 476 PHE A 477 -1 O PHE A 477 N LEU A 41 SHEET 1 AC 5 ASN A 126 ILE A 128 0 SHEET 2 AC 5 LEU A 118 HIS A 123 -1 O CYS A 121 N ILE A 128 SHEET 3 AC 5 ASN A 108 VAL A 112 -1 O LEU A 109 N ALA A 122 SHEET 4 AC 5 LEU A 100 ASP A 103 -1 O VAL A 101 N LEU A 110 SHEET 5 AC 5 PHE A 150 LEU A 153 -1 O TYR A 151 N PHE A 102 SHEET 1 AD 3 THR A 179 CYS A 181 0 SHEET 2 AD 3 GLY A 184 ASP A 187 -1 O GLY A 184 N CYS A 181 SHEET 3 AD 3 LEU A 190 SER A 193 -1 O LEU A 190 N ASP A 187 SHEET 1 AE 2 ARG A 442 SER A 443 0 SHEET 2 AE 2 ARG A 446 GLN A 447 -1 O ARG A 446 N SER A 443 LINK ND2 ASN A 52 MG MG A1492 1555 1555 2.16 LINK O ASP A 54 MG MG A1492 1555 1555 2.11 LINK OD1 ASP A 351 MG MG A1492 1555 1555 2.13 LINK O2P IMP A1491 MG MG A1492 1555 1555 1.93 LINK MG MG A1492 O HOH A2215 1555 1555 2.22 LINK MG MG A1492 O HOH A2218 1555 1555 2.24 CISPEP 1 SER A 62 PRO A 63 0 -1.70 CISPEP 2 LYS A 292 PRO A 293 0 3.46 SITE 1 AC1 4 ARG A 144 LYS A 362 ARG A 456 TYR A 457 SITE 1 AC2 8 PHE A 283 ASP A 284 LEU A 285 ILE A 286 SITE 2 AC2 8 GLN A 322 GLY A 324 ILE A 325 HOH A2256 SITE 1 AC3 18 ASN A 52 MET A 53 ASP A 54 PHE A 157 SITE 2 AC3 18 ARG A 202 ASP A 206 HIS A 209 TYR A 210 SITE 3 AC3 18 LYS A 215 THR A 249 ASN A 250 SER A 251 SITE 4 AC3 18 LYS A 292 MG A1492 HOH A2107 HOH A2215 SITE 5 AC3 18 HOH A2218 HOH A2257 SITE 1 AC4 6 ASN A 52 ASP A 54 ASP A 351 IMP A1491 SITE 2 AC4 6 HOH A2215 HOH A2218 CRYST1 91.570 127.790 130.610 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010921 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007656 0.00000