PDB Short entry for 4MWO HEADER HYDROLASE/HYDROLASE INHIBITOR 25-SEP-13 4MWO TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUCLEOTIDASE TITLE 2 IN COMPLEX WITH THE INHIBITOR CPB-T COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-227; COMPND 5 SYNONYM: 5',3'-NUCLEOTIDASE, MITOCHONDRIAL, DEOXY-5'-NUCLEOTIDASE 2, COMPND 6 DNT-2; COMPND 7 EC: 3.1.3.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DNT1, DNT2, NT5C, NT5M, UMPH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS 5'-NUCLEOTIDASE, PROTEIN CONFORMATION, DEPHOSPHORYLATION, KEYWDS 2 PHOSPHORYLATION, HAD-LIKE, MITOCHONDIA, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,P.REZACOVA,J.BRYNDA REVDAT 3 20-SEP-23 4MWO 1 REMARK SEQADV LINK REVDAT 2 08-OCT-14 4MWO 1 JRNL REVDAT 1 10-SEP-14 4MWO 0 JRNL AUTH O.SIMAK,P.PACHL,M.FABRY,M.BUDESINSKY,T.JANDUSIK,A.HNIZDA, JRNL AUTH 2 R.SKLENICKOVA,M.PETROVA,V.VEVERKA,P.REZACOVA,J.BRYNDA, JRNL AUTH 3 I.ROSENBERG JRNL TITL CONFORMATIONALLY CONSTRAINED NUCLEOSIDE PHOSPHONIC ACIDS - JRNL TITL 2 POTENT INHIBITORS OF HUMAN MITOCHONDRIAL AND CYTOSOLIC JRNL TITL 3 5'(3')-NUCLEOTIDASES. JRNL REF ORG.BIOMOL.CHEM. V. 12 7971 2014 JRNL REFN ISSN 1477-0520 JRNL PMID 25178098 JRNL DOI 10.1039/C4OB01332H REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 34273 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1714 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) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2045 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1585 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : -0.31000 REMARK 3 B33 (A**2) : 0.61000 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): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.623 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1744 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1630 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2382 ; 2.059 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3762 ; 1.390 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 207 ; 5.952 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;28.243 ;22.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 287 ;12.622 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;15.295 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 249 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1936 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 421 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 793 ; 0.849 ; 0.971 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 792 ; 0.847 ; 0.970 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 996 ; 1.281 ; 1.454 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 35 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): -31.7107 4.2277 -22.5220 REMARK 3 T TENSOR REMARK 3 T11: 0.0333 T22: 0.0552 REMARK 3 T33: 0.0683 T12: -0.0262 REMARK 3 T13: -0.0105 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 3.3057 L22: 1.7722 REMARK 3 L33: 1.4480 L12: -0.7790 REMARK 3 L13: 0.8709 L23: -0.4002 REMARK 3 S TENSOR REMARK 3 S11: 0.0234 S12: -0.0384 S13: -0.3231 REMARK 3 S21: -0.1291 S22: 0.0399 S23: 0.3043 REMARK 3 S31: 0.1539 S32: -0.2636 S33: -0.0632 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 107 A 204 REMARK 3 ORIGIN FOR THE GROUP (A): -15.7192 4.7617 -19.1047 REMARK 3 T TENSOR REMARK 3 T11: 0.0075 T22: 0.0034 REMARK 3 T33: 0.0158 T12: 0.0018 REMARK 3 T13: 0.0000 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.0554 L22: 1.5502 REMARK 3 L33: 0.8484 L12: -0.0420 REMARK 3 L13: -0.3154 L23: -0.3846 REMARK 3 S TENSOR REMARK 3 S11: -0.0334 S12: -0.0505 S13: -0.0865 REMARK 3 S21: 0.0048 S22: 0.0059 S23: -0.1036 REMARK 3 S31: 0.0737 S32: 0.0143 S33: 0.0276 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 205 A 227 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0055 -7.1848 -11.5870 REMARK 3 T TENSOR REMARK 3 T11: 0.0804 T22: 0.0885 REMARK 3 T33: 0.1625 T12: -0.0040 REMARK 3 T13: -0.0069 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 4.4664 L22: 4.4753 REMARK 3 L33: 3.8881 L12: -0.4140 REMARK 3 L13: 1.3859 L23: 0.3206 REMARK 3 S TENSOR REMARK 3 S11: 0.0840 S12: 0.2774 S13: -0.3827 REMARK 3 S21: -0.0591 S22: 0.0080 S23: -0.5893 REMARK 3 S31: 0.2746 S32: 0.3070 S33: -0.0920 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 301 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): -24.7168 3.7812 -27.5176 REMARK 3 T TENSOR REMARK 3 T11: 0.1493 T22: 0.1353 REMARK 3 T33: 0.1483 T12: 0.0006 REMARK 3 T13: -0.0285 T23: 0.1073 REMARK 3 L TENSOR REMARK 3 L11: 0.1662 L22: 6.7032 REMARK 3 L33: 0.0034 L12: 0.9263 REMARK 3 L13: 0.0157 L23: 0.1421 REMARK 3 S TENSOR REMARK 3 S11: -0.1178 S12: 0.0850 S13: 0.0931 REMARK 3 S21: -0.8902 S22: 0.1197 S23: 0.1908 REMARK 3 S31: -0.0200 S32: -0.0048 S33: -0.0019 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 4MWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, XDS REMARK 200 DATA SCALING SOFTWARE : SCALA, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34274 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 46.903 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 7.510 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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 4L6A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 8% PEG8000, 10% GLYCEROL, PH 4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 52.97500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.98700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.98700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.46250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.98700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.98700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.48750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.98700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.98700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.46250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.98700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.98700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.48750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.97500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -52.97500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 547 LIES ON A SPECIAL POSITION. 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 SER A 27 REMARK 465 ASN A 28 REMARK 465 ALA A 29 REMARK 465 ALA A 30 REMARK 465 SER A 31 REMARK 465 GLY A 32 REMARK 465 GLY A 33 REMARK 465 ARG A 34 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 134 CD CE NZ 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 ASP A 179 CB ASP A 179 CG 0.130 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 37 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 163 CA - CB - CG ANGL. DEV. = 16.9 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 42 -67.43 -100.22 REMARK 500 VAL A 45 -54.49 -128.19 REMARK 500 SER A 213 170.48 179.66 REMARK 500 REMARK 500 REMARK: NULL 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 K A 304 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 ASP A 43 O 81.8 REMARK 620 3 ASP A 176 OD1 78.6 94.6 REMARK 620 4 2E2 A 301 OBC 130.9 103.2 147.0 REMARK 620 5 PO4 A 302 O3 72.2 88.7 149.9 59.3 REMARK 620 6 GOL A 306 O3 145.1 75.6 77.2 80.6 132.3 REMARK 620 7 HOH A 402 O 83.6 164.4 87.8 82.4 81.8 119.9 REMARK 620 8 HOH A 575 O 154.9 89.8 78.6 74.0 131.4 14.6 105.7 REMARK 620 9 HOH A 576 O 154.6 97.4 126.6 24.4 82.4 56.3 93.5 49.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 303 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 119 O REMARK 620 2 LEU A 121 O 98.6 REMARK 620 3 THR A 124 O 94.9 93.5 REMARK 620 4 HOH A 532 O 90.5 160.0 67.9 REMARK 620 5 HOH A 534 O 170.5 84.6 75.9 83.8 REMARK 620 6 HOH A 548 O 92.4 85.1 172.7 112.5 96.8 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 2E2 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 DBREF 4MWO A 32 227 UNP Q9NPB1 NT5M_HUMAN 32 227 SEQADV 4MWO SER A 27 UNP Q9NPB1 EXPRESSION TAG SEQADV 4MWO ASN A 28 UNP Q9NPB1 EXPRESSION TAG SEQADV 4MWO ALA A 29 UNP Q9NPB1 EXPRESSION TAG SEQADV 4MWO ALA A 30 UNP Q9NPB1 EXPRESSION TAG SEQADV 4MWO SER A 31 UNP Q9NPB1 EXPRESSION TAG SEQRES 1 A 201 SER ASN ALA ALA SER GLY GLY ARG ALA LEU ARG VAL LEU SEQRES 2 A 201 VAL ASP MET ASP GLY VAL LEU ALA ASP PHE GLU GLY GLY SEQRES 3 A 201 PHE LEU ARG LYS PHE ARG ALA ARG PHE PRO ASP GLN PRO SEQRES 4 A 201 PHE ILE ALA LEU GLU ASP ARG ARG GLY PHE TRP VAL SER SEQRES 5 A 201 GLU GLN TYR GLY ARG LEU ARG PRO GLY LEU SER GLU LYS SEQRES 6 A 201 ALA ILE SER ILE TRP GLU SER LYS ASN PHE PHE PHE GLU SEQRES 7 A 201 LEU GLU PRO LEU PRO GLY ALA VAL GLU ALA VAL LYS GLU SEQRES 8 A 201 MET ALA SER LEU GLN ASN THR ASP VAL PHE ILE CYS THR SEQRES 9 A 201 SER PRO ILE LYS MET PHE LYS TYR CYS PRO TYR GLU LYS SEQRES 10 A 201 TYR ALA TRP VAL GLU LYS TYR PHE GLY PRO ASP PHE LEU SEQRES 11 A 201 GLU GLN ILE VAL LEU THR ARG ASP LYS THR VAL VAL SER SEQRES 12 A 201 ALA ASP LEU LEU ILE ASP ASP ARG PRO ASP ILE THR GLY SEQRES 13 A 201 ALA GLU PRO THR PRO SER TRP GLU HIS VAL LEU PHE THR SEQRES 14 A 201 ALA CYS HIS ASN GLN HIS LEU GLN LEU GLN PRO PRO ARG SEQRES 15 A 201 ARG ARG LEU HIS SER TRP ALA ASP ASP TRP LYS ALA ILE SEQRES 16 A 201 LEU ASP SER LYS ARG PRO HET 2E2 A 301 31 HET PO4 A 302 5 HET K A 303 1 HET K A 304 1 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HETNAM 2E2 1-{3,5-O-[(4-CARBOXYPHENYL)(PHOSPHONO)METHYLIDENE]-2- HETNAM 2 2E2 DEOXY-BETA-D-THREO-PENTOFURANOSYL}-5-METHYLPYRIMIDINE- HETNAM 3 2E2 2,4(1H,3H)-DIONE HETNAM PO4 PHOSPHATE ION HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 2E2 C18 H19 N2 O10 P FORMUL 3 PO4 O4 P 3- FORMUL 4 K 2(K 1+) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 HOH *234(H2 O) HELIX 1 1 ASP A 48 PHE A 61 1 14 HELIX 2 2 ALA A 68 ARG A 72 5 5 HELIX 3 3 TRP A 76 ARG A 85 1 10 HELIX 4 4 GLY A 87 GLU A 97 1 11 HELIX 5 5 GLY A 110 LEU A 121 1 12 HELIX 6 6 TYR A 138 GLY A 152 1 15 HELIX 7 7 PRO A 153 GLU A 157 5 5 HELIX 8 8 ASP A 217 ARG A 226 1 10 SHEET 1 A 6 ILE A 159 LEU A 161 0 SHEET 2 A 6 THR A 124 THR A 130 1 N ILE A 128 O VAL A 160 SHEET 3 A 6 LEU A 36 VAL A 40 1 N LEU A 36 O ASP A 125 SHEET 4 A 6 LEU A 172 ASP A 175 1 O LEU A 172 N LEU A 39 SHEET 5 A 6 GLU A 190 PHE A 194 1 O VAL A 192 N LEU A 173 SHEET 6 A 6 ARG A 209 LEU A 211 1 O ARG A 209 N LEU A 193 LINK OD2 ASP A 41 K K A 304 1555 1555 2.49 LINK O ASP A 43 K K A 304 1555 1555 2.28 LINK O ALA A 119 K K A 303 1555 1555 2.53 LINK O LEU A 121 K K A 303 1555 1555 2.60 LINK O THR A 124 K K A 303 1555 1555 2.61 LINK OD1 ASP A 176 K K A 304 1555 1555 2.35 LINK OBCA2E2 A 301 K K A 304 1555 1555 2.60 LINK O3 BPO4 A 302 K K A 304 1555 1555 2.33 LINK K K A 303 O HOH A 532 1555 1555 2.88 LINK K K A 303 O HOH A 534 1555 1555 2.64 LINK K K A 303 O HOH A 548 1555 1555 2.54 LINK K K A 304 O3 CGOL A 306 1555 1555 2.45 LINK K K A 304 O HOH A 402 1555 1555 2.37 LINK K K A 304 O AHOH A 575 1555 1555 2.44 LINK K K A 304 O BHOH A 576 1555 1555 2.54 CISPEP 1 PRO A 206 PRO A 207 0 2.43 SITE 1 AC1 23 ASP A 43 PHE A 49 PHE A 75 TRP A 76 SITE 2 AC1 23 VAL A 77 SER A 78 TRP A 96 SER A 131 SITE 3 AC1 23 PRO A 132 ARG A 163 K A 304 GOL A 306 SITE 4 AC1 23 GOL A 307 HOH A 401 HOH A 528 HOH A 540 SITE 5 AC1 23 HOH A 542 HOH A 549 HOH A 554 HOH A 575 SITE 6 AC1 23 HOH A 576 HOH A 633 HOH A 634 SITE 1 AC2 12 ASP A 41 MET A 42 ASP A 43 THR A 130 SITE 2 AC2 12 SER A 131 LYS A 143 LYS A 165 K A 304 SITE 3 AC2 12 HOH A 401 HOH A 402 HOH A 528 HOH A 549 SITE 1 AC3 6 ALA A 119 LEU A 121 THR A 124 HOH A 532 SITE 2 AC3 6 HOH A 534 HOH A 548 SITE 1 AC4 9 ASP A 41 ASP A 43 ASP A 176 2E2 A 301 SITE 2 AC4 9 PO4 A 302 GOL A 306 HOH A 402 HOH A 575 SITE 3 AC4 9 HOH A 576 SITE 1 AC5 3 PRO A 65 PHE A 66 HOH A 482 SITE 1 AC6 14 ASP A 43 GLU A 50 ARG A 72 PHE A 75 SITE 2 AC6 14 VAL A 77 ASP A 176 HIS A 198 2E2 A 301 SITE 3 AC6 14 K A 304 HOH A 422 HOH A 575 HOH A 576 SITE 4 AC6 14 HOH A 578 HOH A 634 SITE 1 AC7 7 ARG A 163 ARG A 177 THR A 181 2E2 A 301 SITE 2 AC7 7 HOH A 418 HOH A 454 HOH A 561 CRYST1 73.974 73.974 105.950 90.00 90.00 90.00 P 43 21 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 0.013518 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009438 0.00000