PDB Short entry for 4OI0 HEADER RNA BINDING PROTEIN/RNA 18-JAN-14 4OI0 TITLE BOUND TO SSRNA DINUCLEOTIDE GC, ADP, ALF4-, AND MG2+(TRANSITION STATE, TITLE 2 DATA SET I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CLPF-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*GP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: DIRIBONUCLEOTIDE GC SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: CLPF-1, F59A2.4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS POLYNUCLEOTIDE KINASE, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.DIKFIDAN,B.LOLL,C.ZEYMER,T.CLAUSEN,A.MEINHART REVDAT 5 28-FEB-24 4OI0 1 REMARK SEQADV LINK REVDAT 4 22-NOV-17 4OI0 1 REMARK REVDAT 3 21-JAN-15 4OI0 1 TITLE REVDAT 2 02-JUL-14 4OI0 1 JRNL REVDAT 1 14-MAY-14 4OI0 0 JRNL AUTH A.DIKFIDAN,B.LOLL,C.ZEYMER,I.MAGLER,T.CLAUSEN,A.MEINHART JRNL TITL RNA SPECIFICITY AND REGULATION OF CATALYSIS IN THE JRNL TITL 2 EUKARYOTIC POLYNUCLEOTIDE KINASE CLP1. JRNL REF MOL.CELL V. 54 975 2014 JRNL REFN ISSN 1097-2765 JRNL PMID 24813946 JRNL DOI 10.1016/J.MOLCEL.2014.04.005 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21145 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1108 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1223 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.5620 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.5770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3096 REMARK 3 NUCLEIC ACID ATOMS : 40 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.22000 REMARK 3 B12 (A**2) : -0.07000 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): 0.340 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.251 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.481 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.887 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3331 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2246 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4534 ; 1.155 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5514 ; 0.792 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 421 ; 5.718 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;35.607 ;24.406 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 579 ;13.431 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.614 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 525 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3639 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 654 ; 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): 2022 ; 0.412 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 824 ; 0.083 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3290 ; 0.779 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1309 ; 1.203 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1231 ; 1.989 ; 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 : 3 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 4 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): -2.5975 15.0663 -4.5305 REMARK 3 T TENSOR REMARK 3 T11: 0.1935 T22: 0.0284 REMARK 3 T33: 0.0249 T12: 0.0557 REMARK 3 T13: 0.0226 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 11.8994 L22: 1.5016 REMARK 3 L33: 2.3553 L12: -0.8433 REMARK 3 L13: -1.3695 L23: -0.3709 REMARK 3 S TENSOR REMARK 3 S11: -0.2834 S12: -0.0452 S13: 0.2718 REMARK 3 S21: 0.1555 S22: 0.1532 S23: 0.0050 REMARK 3 S31: 0.0512 S32: 0.0497 S33: 0.1302 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 111 A 310 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1330 25.7282 5.0976 REMARK 3 T TENSOR REMARK 3 T11: 0.0946 T22: 0.0865 REMARK 3 T33: 0.0471 T12: 0.0229 REMARK 3 T13: 0.0290 T23: -0.0098 REMARK 3 L TENSOR REMARK 3 L11: 1.2145 L22: 3.1438 REMARK 3 L33: 2.1761 L12: -0.5399 REMARK 3 L13: -0.2481 L23: 0.3239 REMARK 3 S TENSOR REMARK 3 S11: 0.0238 S12: 0.0076 S13: 0.1414 REMARK 3 S21: 0.0688 S22: -0.0456 S23: 0.0642 REMARK 3 S31: -0.1421 S32: -0.2279 S33: 0.0218 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 311 A 423 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9119 51.7238 6.1949 REMARK 3 T TENSOR REMARK 3 T11: 0.2449 T22: 0.0719 REMARK 3 T33: 0.3189 T12: 0.0636 REMARK 3 T13: 0.0324 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 4.1992 L22: 6.5264 REMARK 3 L33: 4.5438 L12: 0.6224 REMARK 3 L13: 0.1789 L23: 0.2119 REMARK 3 S TENSOR REMARK 3 S11: -0.1119 S12: -0.1566 S13: 0.6506 REMARK 3 S21: -0.0227 S22: 0.1611 S23: 0.2428 REMARK 3 S31: -0.4480 S32: -0.2357 S33: -0.0492 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4OI0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC KB MIRRORS REMARK 200 OPTICS : RIGAKU VARIMAX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22553 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NONE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DIFFRACTION DATA INCLUDE DEBY-SCHERRER RINGS AT 3.62 REMARK 200 ANGSTROM AND 2.25 ANGSTROM RESOLUTION FROM SALT IN THE CRYO REMARK 200 SOLUTION REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA2HPO4/KH2PO4 200 MM NACL 15 REMARK 280 MM MGCL2 90 MM SARCOSINE 25% (W/V) PEG 1000, PH 5.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.46667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.93333 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: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 106 REMARK 465 GLY A 107 REMARK 465 ASN A 108 REMARK 465 SER A 109 REMARK 465 ASN A 110 REMARK 465 ALA A 332 REMARK 465 GLU A 333 REMARK 465 GLN A 334 REMARK 465 LEU A 335 REMARK 465 PRO A 336 REMARK 465 ASP A 337 REMARK 465 SER A 338 REMARK 465 CYS A 339 REMARK 465 LEU A 340 REMARK 465 PRO A 341 REMARK 465 PHE A 342 REMARK 465 GLY A 343 REMARK 465 MET A 344 REMARK 465 GLU A 345 REMARK 465 VAL A 346 REMARK 465 GLU A 347 REMARK 465 ASN A 348 REMARK 465 HIS A 349 REMARK 465 GLU A 350 REMARK 465 ASP A 424 REMARK 465 GLN A 425 REMARK 465 ILE A 426 REMARK 465 LYS A 427 REMARK 465 ARG A 428 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O3B ADP A 501 AL ALF A 503 2.00 REMARK 500 O5' G B 1 AL ALF A 503 2.16 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 PHE A 39 46.78 38.20 REMARK 500 LYS A 54 -15.11 73.11 REMARK 500 ALA A 76 118.97 -167.89 REMARK 500 ASN A 196 82.98 -162.32 REMARK 500 HIS A 364 -2.24 78.22 REMARK 500 ASP A 376 -155.41 -128.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE A 506 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 A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 128 OG1 REMARK 620 2 ADP A 501 O2B 92.9 REMARK 620 3 HOH A 601 O 81.1 173.0 REMARK 620 4 HOH A 602 O 92.7 101.9 82.1 REMARK 620 5 HOH A 603 O 85.6 86.2 89.8 171.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALF A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAR A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAR A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OHV RELATED DB: PDB REMARK 900 RELATED ID: 4OHW RELATED DB: PDB REMARK 900 RELATED ID: 4OHX RELATED DB: PDB REMARK 900 RELATED ID: 4OHY RELATED DB: PDB REMARK 900 RELATED ID: 4OHZ RELATED DB: PDB REMARK 900 RELATED ID: 4OI1 RELATED DB: PDB REMARK 900 RELATED ID: 4OI2 RELATED DB: PDB DBREF 4OI0 A 1 428 UNP P52874 CLP1_CAEEL 1 428 DBREF 4OI0 B 1 2 PDB 4OI0 4OI0 1 2 SEQADV 4OI0 GLY A -2 UNP P52874 EXPRESSION TAG SEQADV 4OI0 SER A -1 UNP P52874 EXPRESSION TAG SEQADV 4OI0 HIS A 0 UNP P52874 EXPRESSION TAG SEQRES 1 A 431 GLY SER HIS MET SER GLU GLU ASN VAL GLN GLU PHE VAL SEQRES 2 A 431 LEU LYS GLU ASP CYS GLU LEU ARG PHE ALA ALA GLY ASP SEQRES 3 A 431 ASP SER ASP VAL CYS LEU GLU LEU VAL LYS GLY TYR ALA SEQRES 4 A 431 GLU ILE PHE GLY THR GLU LEU LEU LEU ASN LYS LYS TYR SEQRES 5 A 431 THR PHE PRO ALA LYS SER ARG VAL ALA ALA PHE THR TRP SEQRES 6 A 431 LYS GLY ALA THR ILE GLU LEU VAL GLY THR THR GLU SER SEQRES 7 A 431 ALA TYR VAL ALA GLU SER THR PRO MET VAL ILE TYR LEU SEQRES 8 A 431 ASN ILE HIS ALA ALA MET GLU GLU VAL ARG LYS LYS ARG SEQRES 9 A 431 GLU GLU GLN ALA ALA GLY ASN SER ASN LYS ALA LYS GLY SEQRES 10 A 431 PRO ARG LEU LEU LEU VAL GLY PRO THR ASP VAL GLY LYS SEQRES 11 A 431 THR THR VAL SER ARG ILE LEU CYS ASN TYR SER VAL ARG SEQRES 12 A 431 GLN GLY ARG THR PRO ILE PHE VAL GLU LEU ASP VAL GLY SEQRES 13 A 431 GLN ASN SER VAL SER VAL PRO GLY THR VAL ALA ALA VAL SEQRES 14 A 431 LEU VAL GLN LYS THR ALA ASP VAL ILE ASP GLY PHE GLU SEQRES 15 A 431 ARG ASN GLN PRO ILE VAL PHE ASN PHE GLY HIS THR SER SEQRES 16 A 431 PRO SER ALA ASN LEU SER LEU TYR GLU ALA LEU PHE LYS SEQRES 17 A 431 GLU MET ALA THR THR LEU ASN ALA GLN ILE GLN GLU ASN SEQRES 18 A 431 ASP GLU ALA LYS ILE GLY GLY MET ILE ILE ASN THR CYS SEQRES 19 A 431 GLY TRP VAL ASP GLY GLU GLY TYR LYS CYS ILE VAL LYS SEQRES 20 A 431 ALA ALA SER ALA PHE GLU VAL ASP VAL VAL ILE VAL LEU SEQRES 21 A 431 ASP HIS GLU ARG LEU TYR SER ASP LEU SER LYS GLU LEU SEQRES 22 A 431 PRO GLU PHE VAL ARG LEU THR HIS VAL PRO LYS SER GLY SEQRES 23 A 431 GLY VAL GLU GLN ARG THR GLY GLN ILE ARG SER LYS MET SEQRES 24 A 431 ARG GLY GLU ASN VAL HIS ARG TYR PHE TYR GLY THR ARG SEQRES 25 A 431 ALA ASN ASN LEU TYR PRO PHE THR PHE ASP VAL SER PHE SEQRES 26 A 431 ASP ASP VAL THR LEU CYS LYS ILE GLY ALA GLU GLN LEU SEQRES 27 A 431 PRO ASP SER CYS LEU PRO PHE GLY MET GLU VAL GLU ASN SEQRES 28 A 431 HIS GLU THR LYS LEU VAL ILE MET GLU PRO SER ALA ASP SEQRES 29 A 431 ILE LYS HIS HIS LEU PHE ALA PHE SER ARG SER THR LYS SEQRES 30 A 431 ALA ASP GLU ASN VAL LEU LYS SER PRO VAL PHE GLY PHE SEQRES 31 A 431 CYS LEU VAL THR GLU VAL ASP LEU GLU LYS ARG THR MET SEQRES 32 A 431 SER ILE LEU CYS PRO GLN ARG THR ILE PRO SER LYS VAL SEQRES 33 A 431 LEU VAL PHE SER ASP ILE THR HIS LEU ASP ASP GLN ILE SEQRES 34 A 431 LYS ARG SEQRES 1 B 2 G C HET ADP A 501 27 HET MG A 502 1 HET ALF A 503 5 HET SAR A 504 6 HET SAR A 505 6 HET 2PE A 506 13 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ALF TETRAFLUOROALUMINATE ION HETNAM SAR SARCOSINE HETNAM 2PE NONAETHYLENE GLYCOL FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG MG 2+ FORMUL 5 ALF AL F4 1- FORMUL 6 SAR 2(C3 H7 N O2) FORMUL 8 2PE C18 H38 O10 FORMUL 9 HOH *135(H2 O) HELIX 1 1 PRO A 83 ALA A 105 1 23 HELIX 2 2 GLY A 126 GLN A 141 1 16 HELIX 3 3 SER A 192 ALA A 195 5 4 HELIX 4 4 ASN A 196 ILE A 215 1 20 HELIX 5 5 ASN A 218 GLY A 225 1 8 HELIX 6 6 GLY A 236 PHE A 249 1 14 HELIX 7 7 HIS A 259 LEU A 270 1 12 HELIX 8 8 THR A 289 GLY A 307 1 19 HELIX 9 9 ASP A 323 VAL A 325 5 3 HELIX 10 10 SER A 359 LYS A 363 5 5 SHEET 1 A 4 VAL A 6 LEU A 11 0 SHEET 2 A 4 ALA A 65 VAL A 70 -1 O ALA A 65 N LEU A 11 SHEET 3 A 4 VAL A 27 GLY A 34 -1 N CYS A 28 O VAL A 70 SHEET 4 A 4 LYS A 48 PHE A 51 -1 O PHE A 51 N VAL A 27 SHEET 1 B 5 THR A 41 GLU A 42 0 SHEET 2 B 5 GLU A 37 ILE A 38 -1 N ILE A 38 O THR A 41 SHEET 3 B 5 ARG A 56 THR A 61 -1 O PHE A 60 N GLU A 37 SHEET 4 B 5 CYS A 15 ALA A 21 -1 N PHE A 19 O VAL A 57 SHEET 5 B 5 THR A 73 ALA A 79 -1 O ALA A 79 N GLU A 16 SHEET 1 C 7 ILE A 184 ASN A 187 0 SHEET 2 C 7 THR A 162 LEU A 167 -1 N ALA A 165 O ILE A 184 SHEET 3 C 7 ILE A 146 GLU A 149 -1 N PHE A 147 O VAL A 166 SHEET 4 C 7 MET A 226 ASN A 229 1 O ASN A 229 N VAL A 148 SHEET 5 C 7 ARG A 116 VAL A 120 1 N LEU A 117 O ILE A 228 SHEET 6 C 7 VAL A 253 LEU A 257 1 O ILE A 255 N LEU A 118 SHEET 7 C 7 ARG A 275 VAL A 279 1 O THR A 277 N VAL A 254 SHEET 1 D 7 PHE A 316 SER A 321 0 SHEET 2 D 7 THR A 399 CYS A 404 -1 O CYS A 404 N PHE A 316 SHEET 3 D 7 VAL A 384 ASP A 394 -1 N ASP A 394 O THR A 399 SHEET 4 D 7 HIS A 365 SER A 370 -1 N PHE A 369 O PHE A 385 SHEET 5 D 7 VAL A 413 THR A 420 -1 O VAL A 415 N ALA A 368 SHEET 6 D 7 THR A 326 ILE A 330 1 N CYS A 328 O PHE A 416 SHEET 7 D 7 LEU A 353 ILE A 355 -1 O VAL A 354 N LYS A 329 LINK OG1 THR A 128 MG MG A 502 1555 1555 2.21 LINK O2B ADP A 501 MG MG A 502 1555 1555 1.99 LINK MG MG A 502 O HOH A 601 1555 1555 2.12 LINK MG MG A 502 O HOH A 602 1555 1555 2.01 LINK MG MG A 502 O HOH A 603 1555 1555 2.15 SITE 1 AC1 20 GLU A 16 ARG A 56 ALA A 58 ASP A 124 SITE 2 AC1 20 VAL A 125 GLY A 126 LYS A 127 THR A 128 SITE 3 AC1 20 THR A 129 SER A 282 GLY A 284 GLU A 286 SITE 4 AC1 20 ARG A 288 MG A 502 ALF A 503 HOH A 602 SITE 5 AC1 20 HOH A 603 HOH A 613 HOH A 628 HOH A 698 SITE 1 AC2 6 THR A 128 ADP A 501 ALF A 503 HOH A 601 SITE 2 AC2 6 HOH A 602 HOH A 603 SITE 1 AC3 14 THR A 123 ASP A 124 LYS A 127 ASP A 151 SITE 2 AC3 14 GLN A 154 GLY A 232 ARG A 288 ARG A 293 SITE 3 AC3 14 ADP A 501 MG A 502 HOH A 601 HOH A 602 SITE 4 AC3 14 HOH A 603 G B 1 SITE 1 AC4 2 TYR A 77 HOH A 706 SITE 1 AC5 2 GLN A 182 HOH A 692 SITE 1 AC6 3 TRP A 62 LEU A 88 TYR A 137 CRYST1 100.710 100.710 40.400 90.00 90.00 120.00 P 31 3 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 0.009930 0.005733 0.000000 0.00000 SCALE2 0.000000 0.011466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024752 0.00000