HEADER ADP BINDING PROTEIN 09-SEP-12 3VX3 TITLE CRYSTAL STRUCTURE OF [NIFE] HYDROGENASE MATURATION PROTEIN HYPB FROM TITLE 2 THERMOCOCCUS KODAKARENSIS KOD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE INVOLVED IN CHROMOSOME PARTITIONING, PARA/MIND COMPND 3 FAMILY, MRP HOMOLOG; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 5 GENE: TK2007; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A(+) KEYWDS MRP/MIND FAMILY ATPASE, [NIFE] HYDROGENASE MATURATION, ADP BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.SASAKI,S.WATANABE,K.MIKI REVDAT 3 20-MAR-24 3VX3 1 REMARK REVDAT 2 12-JUN-13 3VX3 1 JRNL REVDAT 1 27-FEB-13 3VX3 0 JRNL AUTH D.SASAKI,S.WATANABE,R.MATSUMI,T.SHOJI,A.YASUKOCHI, JRNL AUTH 2 K.TAGASHIRA,W.FUKUDA,T.KANAI,H.ATOMI,T.IMANAKA,K.MIKI JRNL TITL IDENTIFICATION AND STRUCTURE OF A NOVEL ARCHAEAL HYPB FOR JRNL TITL 2 [NIFE] HYDROGENASE MATURATION JRNL REF J.MOL.BIOL. V. 425 1627 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23399544 JRNL DOI 10.1016/J.JMB.2013.02.004 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38324 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2766 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 159 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3678 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.98000 REMARK 3 B22 (A**2) : 0.22000 REMARK 3 B33 (A**2) : 1.77000 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): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.403 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3816 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5154 ; 1.497 ; 2.031 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 464 ; 5.979 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;33.251 ;23.867 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 696 ;14.838 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.933 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2738 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2326 ; 0.699 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3766 ; 1.286 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1490 ; 2.101 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1388 ; 3.449 ; 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 : 2 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 248 REMARK 3 ORIGIN FOR THE GROUP (A): -14.8587 -13.7326 -17.6177 REMARK 3 T TENSOR REMARK 3 T11: 0.0669 T22: 0.1182 REMARK 3 T33: 0.1068 T12: 0.0245 REMARK 3 T13: -0.0116 T23: -0.1018 REMARK 3 L TENSOR REMARK 3 L11: 1.0722 L22: 2.9019 REMARK 3 L33: 2.5321 L12: 0.2919 REMARK 3 L13: 0.0590 L23: 1.0293 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: 0.0196 S13: -0.0791 REMARK 3 S21: 0.1107 S22: 0.1000 S23: -0.2780 REMARK 3 S31: 0.0327 S32: 0.0716 S33: -0.1186 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 : B 4 B 248 REMARK 3 ORIGIN FOR THE GROUP (A): -40.4321 -23.3619 -27.5738 REMARK 3 T TENSOR REMARK 3 T11: 0.0723 T22: 0.0986 REMARK 3 T33: 0.1285 T12: 0.0010 REMARK 3 T13: -0.0205 T23: -0.1086 REMARK 3 L TENSOR REMARK 3 L11: 2.8297 L22: 2.3203 REMARK 3 L33: 1.1620 L12: -0.4087 REMARK 3 L13: -0.1404 L23: 0.9301 REMARK 3 S TENSOR REMARK 3 S11: -0.0474 S12: 0.0951 S13: -0.1338 REMARK 3 S21: -0.0510 S22: 0.0066 S23: 0.0957 REMARK 3 S31: 0.0839 S32: -0.0317 S33: 0.0408 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 3VX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000095608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40492 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.52900 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE/POTASSIUM PHOSPHATE DIBASIC, PH 5.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.0K 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 33.12050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.84450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.41050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.12050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.84450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.41050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.12050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.84450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.41050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.12050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.84450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.41050 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: 5340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 99 REMARK 465 ASP A 100 REMARK 465 ARG A 101 REMARK 465 PRO A 102 REMARK 465 SER A 192 REMARK 465 GLU A 193 REMARK 465 GLN A 194 REMARK 465 LEU A 195 REMARK 465 ASP A 196 REMARK 465 ASP A 197 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ALA B 3 REMARK 465 GLU B 99 REMARK 465 ASP B 100 REMARK 465 ARG B 101 REMARK 465 PRO B 102 REMARK 465 SER B 192 REMARK 465 GLU B 193 REMARK 465 GLN B 194 REMARK 465 LEU B 195 REMARK 465 ASP B 196 REMARK 465 ASP B 197 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 O HOH A 463 O HOH A 488 2.04 REMARK 500 OH TYR B 97 O2 EDO B 304 2.14 REMARK 500 O HOH B 453 O HOH B 468 2.14 REMARK 500 O HOH B 440 O HOH B 445 2.17 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 B 150 NE - CZ - NH2 ANGL. DEV. = -3.6 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 LYS A 72 -99.95 -125.79 REMARK 500 ASP A 124 -138.30 55.33 REMARK 500 LYS B 72 -104.95 -74.73 REMARK 500 ASP B 124 -126.45 52.23 REMARK 500 REMARK 500 REMARK: NULL 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 304 DBREF 3VX3 A 1 248 UNP Q5JIH4 Q5JIH4_PYRKO 1 248 DBREF 3VX3 B 1 248 UNP Q5JIH4 Q5JIH4_PYRKO 1 248 SEQRES 1 A 248 MET ASN ALA ILE ASP PRO ARG GLU ILE ALA ILE ASN ALA SEQRES 2 A 248 ARG LEU GLU GLY VAL LYS ARG ILE ILE PRO VAL VAL SER SEQRES 3 A 248 GLY LYS GLY GLY VAL GLY LYS SER LEU VAL SER THR THR SEQRES 4 A 248 LEU ALA LEU VAL LEU ALA GLU LYS GLY TYR ARG VAL GLY SEQRES 5 A 248 LEU LEU ASP LEU ASP PHE HIS GLY ALA SER ASP HIS VAL SEQRES 6 A 248 ILE LEU GLY PHE GLU PRO LYS GLU PHE PRO GLU GLU ASP SEQRES 7 A 248 ARG GLY VAL VAL PRO PRO THR VAL HIS GLY ILE LYS PHE SEQRES 8 A 248 MET THR ILE ALA TYR TYR THR GLU ASP ARG PRO THR PRO SEQRES 9 A 248 LEU ARG GLY LYS GLU ILE SER ASP ALA LEU ILE GLU LEU SEQRES 10 A 248 LEU THR ILE THR ARG TRP ASP GLU LEU ASP TYR LEU VAL SEQRES 11 A 248 ILE ASP MET PRO PRO GLY LEU GLY ASP GLN LEU LEU ASP SEQRES 12 A 248 VAL LEU ARG PHE LEU LYS ARG GLY GLU PHE LEU VAL VAL SEQRES 13 A 248 ALA THR PRO SER LYS LEU SER LEU ASN VAL VAL ARG LYS SEQRES 14 A 248 LEU ILE GLU LEU LEU LYS GLU GLU GLY HIS LYS VAL ILE SEQRES 15 A 248 GLY VAL VAL GLU ASN MET LYS LEU ARG SER GLU GLN LEU SEQRES 16 A 248 ASP ASP GLU LYS ASP VAL GLU LYS LEU ALA GLU GLU PHE SEQRES 17 A 248 GLY VAL PRO TYR LEU VAL GLY ILE PRO PHE TYR PRO ASP SEQRES 18 A 248 LEU ASP ALA LYS VAL GLY ASN VAL GLU GLU LEU MET LYS SEQRES 19 A 248 THR GLU PHE ALA GLY LYS VAL ARG GLU LEU ALA GLY ARG SEQRES 20 A 248 LEU SEQRES 1 B 248 MET ASN ALA ILE ASP PRO ARG GLU ILE ALA ILE ASN ALA SEQRES 2 B 248 ARG LEU GLU GLY VAL LYS ARG ILE ILE PRO VAL VAL SER SEQRES 3 B 248 GLY LYS GLY GLY VAL GLY LYS SER LEU VAL SER THR THR SEQRES 4 B 248 LEU ALA LEU VAL LEU ALA GLU LYS GLY TYR ARG VAL GLY SEQRES 5 B 248 LEU LEU ASP LEU ASP PHE HIS GLY ALA SER ASP HIS VAL SEQRES 6 B 248 ILE LEU GLY PHE GLU PRO LYS GLU PHE PRO GLU GLU ASP SEQRES 7 B 248 ARG GLY VAL VAL PRO PRO THR VAL HIS GLY ILE LYS PHE SEQRES 8 B 248 MET THR ILE ALA TYR TYR THR GLU ASP ARG PRO THR PRO SEQRES 9 B 248 LEU ARG GLY LYS GLU ILE SER ASP ALA LEU ILE GLU LEU SEQRES 10 B 248 LEU THR ILE THR ARG TRP ASP GLU LEU ASP TYR LEU VAL SEQRES 11 B 248 ILE ASP MET PRO PRO GLY LEU GLY ASP GLN LEU LEU ASP SEQRES 12 B 248 VAL LEU ARG PHE LEU LYS ARG GLY GLU PHE LEU VAL VAL SEQRES 13 B 248 ALA THR PRO SER LYS LEU SER LEU ASN VAL VAL ARG LYS SEQRES 14 B 248 LEU ILE GLU LEU LEU LYS GLU GLU GLY HIS LYS VAL ILE SEQRES 15 B 248 GLY VAL VAL GLU ASN MET LYS LEU ARG SER GLU GLN LEU SEQRES 16 B 248 ASP ASP GLU LYS ASP VAL GLU LYS LEU ALA GLU GLU PHE SEQRES 17 B 248 GLY VAL PRO TYR LEU VAL GLY ILE PRO PHE TYR PRO ASP SEQRES 18 B 248 LEU ASP ALA LYS VAL GLY ASN VAL GLU GLU LEU MET LYS SEQRES 19 B 248 THR GLU PHE ALA GLY LYS VAL ARG GLU LEU ALA GLY ARG SEQRES 20 B 248 LEU HET ADP A 301 27 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET ADP B 301 27 HET EDO B 302 4 HET EDO B 303 4 HET EDO B 304 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 EDO 6(C2 H6 O2) FORMUL 11 HOH *175(H2 O) HELIX 1 1 ASP A 5 GLU A 16 1 12 HELIX 2 2 GLY A 32 LYS A 47 1 16 HELIX 3 3 SER A 62 LEU A 67 1 6 HELIX 4 4 ALA A 95 TYR A 97 5 3 HELIX 5 5 ARG A 106 THR A 121 1 16 HELIX 6 6 GLY A 138 ARG A 146 1 9 HELIX 7 7 SER A 163 GLU A 177 1 15 HELIX 8 8 LYS A 199 PHE A 208 1 10 HELIX 9 9 ASP A 221 VAL A 226 1 6 HELIX 10 10 ASN A 228 MET A 233 1 6 HELIX 11 11 THR A 235 GLY A 246 1 12 HELIX 12 12 ASP B 5 GLU B 16 1 12 HELIX 13 13 GLY B 32 LYS B 47 1 16 HELIX 14 14 SER B 62 LEU B 67 1 6 HELIX 15 15 ALA B 95 THR B 98 5 4 HELIX 16 16 GLY B 107 THR B 121 1 15 HELIX 17 17 GLY B 138 ARG B 146 1 9 HELIX 18 18 SER B 160 LEU B 162 5 3 HELIX 19 19 SER B 163 GLU B 177 1 15 HELIX 20 20 LYS B 199 PHE B 208 1 10 HELIX 21 21 ASP B 221 LYS B 225 5 5 HELIX 22 22 ASN B 228 THR B 235 1 8 HELIX 23 23 THR B 235 ARG B 247 1 13 SHEET 1 A 8 THR A 85 VAL A 86 0 SHEET 2 A 8 ILE A 89 THR A 93 -1 O ILE A 89 N VAL A 86 SHEET 3 A 8 VAL A 51 ASP A 55 1 N LEU A 53 O LYS A 90 SHEET 4 A 8 LEU A 126 ASP A 132 1 O TYR A 128 N GLY A 52 SHEET 5 A 8 VAL A 18 SER A 26 1 N ILE A 22 O LEU A 129 SHEET 6 A 8 GLU A 152 ALA A 157 1 O VAL A 156 N VAL A 25 SHEET 7 A 8 LYS A 180 LYS A 189 1 O ASN A 187 N ALA A 157 SHEET 8 A 8 TYR A 212 PRO A 217 1 O ILE A 216 N GLU A 186 SHEET 1 B 2 GLU A 76 GLU A 77 0 SHEET 2 B 2 GLY A 80 VAL A 81 -1 O GLY A 80 N GLU A 77 SHEET 1 C 8 THR B 85 VAL B 86 0 SHEET 2 C 8 ILE B 89 THR B 93 -1 O ILE B 89 N VAL B 86 SHEET 3 C 8 VAL B 51 ASP B 55 1 N LEU B 53 O LYS B 90 SHEET 4 C 8 LEU B 126 ASP B 132 1 O VAL B 130 N GLY B 52 SHEET 5 C 8 VAL B 18 SER B 26 1 N VAL B 24 O ILE B 131 SHEET 6 C 8 GLU B 152 ALA B 157 1 O LEU B 154 N VAL B 25 SHEET 7 C 8 LYS B 180 LYS B 189 1 O ASN B 187 N ALA B 157 SHEET 8 C 8 TYR B 212 PRO B 217 1 O ILE B 216 N GLU B 186 CISPEP 1 THR B 103 PRO B 104 0 16.37 SITE 1 AC1 17 GLY A 30 VAL A 31 GLY A 32 LYS A 33 SITE 2 AC1 17 SER A 34 LEU A 35 ASN A 187 PRO A 217 SITE 3 AC1 17 PHE A 218 TYR A 219 ASP A 223 HOH A 411 SITE 4 AC1 17 HOH A 414 HOH A 436 LYS B 28 SER B 160 SITE 5 AC1 17 LEU B 162 SITE 1 AC2 4 LYS A 28 GLY A 29 LYS B 28 GLY B 29 SITE 1 AC3 6 ASP A 139 HOH A 473 GLY B 107 ILE B 110 SITE 2 AC3 6 ASP B 139 GLN B 140 SITE 1 AC4 4 GLY A 68 GLY A 227 ASN A 228 HOH A 470 SITE 1 AC5 22 LYS A 28 SER A 160 LEU A 162 GLY B 29 SITE 2 AC5 22 GLY B 30 VAL B 31 GLY B 32 LYS B 33 SITE 3 AC5 22 SER B 34 LEU B 35 ASN B 187 MET B 188 SITE 4 AC5 22 PRO B 217 PHE B 218 TYR B 219 ASP B 223 SITE 5 AC5 22 VAL B 226 HOH B 408 HOH B 414 HOH B 422 SITE 6 AC5 22 HOH B 433 HOH B 443 SITE 1 AC6 7 TYR B 219 PRO B 220 ASP B 221 LEU B 222 SITE 2 AC6 7 LYS B 225 HOH B 415 HOH B 463 SITE 1 AC7 4 LYS B 175 LYS B 180 VAL B 181 GLY B 209 SITE 1 AC8 6 GLU A 176 TYR B 97 ALA B 113 GLU B 116 SITE 2 AC8 6 LEU B 117 ILE B 120 CRYST1 66.241 137.689 150.821 90.00 90.00 90.00 I 2 2 2 16 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 0.015096 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007263 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006630 0.00000