PDB Short entry for 1VK1 HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 13-APR-04 1VK1 TITLE CONSERVED HYPOTHETICAL PROTEIN FROM PYROCOCCUS FURIOSUS PFU-392566-001 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS REDUCTIVE METHYLATION, DIMETHYL LYSINE, PYROCOCCUS FURIOSUS, KEYWDS 2 CONSERVED HYPOTHETICAL PROTEIN, STRUCTURAL GENOMICS, PSI, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, SOUTHEAST COLLABORATORY FOR STRUCTURAL KEYWDS 4 GENOMICS, SECSG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.SHAH,Z.J.LIU,W.TEMPEL,L.CHEN,D.LEE,H.YANG,J.CHANG,M.ZHAO,J.NG, AUTHOR 2 J.ROSE,P.S.BRERETON,M.IZUMI,F.E.JENNEY JR.,F.L.POOLE II,C.SHAH, AUTHOR 3 F.J.SUGAR,M.W.W.ADAMS,D.C.RICHARDSON,J.S.RICHARDSON,B.C.WANG, AUTHOR 4 SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 7 27-DEC-23 1VK1 1 REMARK SEQADV LINK REVDAT 6 04-OCT-17 1VK1 1 REMARK REVDAT 5 09-JAN-13 1VK1 1 JRNL REMARK VERSN REVDAT 4 09-DEC-08 1VK1 1 JRNL VERSN REVDAT 3 08-FEB-05 1VK1 1 HEADER REVDAT 2 01-FEB-05 1VK1 1 AUTHOR KEYWDS REMARK REVDAT 1 10-AUG-04 1VK1 0 JRNL AUTH N.SHAW,C.CHENG,W.TEMPEL,J.CHANG,J.NG,X.Y.WANG,S.PERRETT, JRNL AUTH 2 J.ROSE,Z.RAO,B.C.WANG,Z.J.LIU JRNL TITL (NZ)CH...O CONTACTS ASSIST CRYSTALLIZATION OF A PARB-LIKE JRNL TITL 2 NUCLEASE. JRNL REF BMC STRUCT.BIOL. V. 7 46 2007 JRNL REFN ESSN 1472-6807 JRNL PMID 17617922 JRNL DOI 10.1186/1472-6807-7-46 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.SHAW,W.TEMPEL,J.CHANG,H.YANG,C.CHENG,J.NG,J.ROSE,Z.RAO, REMARK 1 AUTH 2 B.C.WANG,Z.J.LIU REMARK 1 TITL CRYSTAL STRUCTURE SOLUTION OF A PARB-LIKE NUCLEASE AT ATOMIC REMARK 1 TITL 2 RESOLUTION. REMARK 1 REF PROTEINS V. 70 263 2008 REMARK 1 REFN ISSN 0887-3585 REMARK 1 PMID 17729285 REMARK 1 DOI 10.1002/PROT.21641 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0001 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 63181 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3374 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1369 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.1940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1843 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : 1.12000 REMARK 3 B33 (A**2) : -1.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1914 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1855 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2586 ; 1.298 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4288 ; 0.740 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 5.951 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;30.568 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 352 ;10.971 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;13.897 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 285 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2050 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 358 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 310 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1779 ; 0.166 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1173 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 77 ; 0.094 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.162 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.084 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.206 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.163 ; 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): 1159 ; 1.991 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 471 ; 1.790 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1877 ; 2.792 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 755 ; 2.514 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 709 ; 3.701 ; 3.000 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): 3769 ; 1.301 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 138 ; 6.374 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3732 ; 3.239 ; 3.000 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 : BABINET MODEL WITH 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 1VK1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000001936. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 80.5 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 21.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SINGLE WAVELENGTH REMARK 200 ANOMALOUS SCATTERING REMARK 200 SOFTWARE USED: SOLVE 2.03, RESOLVE 2.03, SCA2STRUCTURE PIPELINE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M NACL, 0.1M TRIS, PH 8.5, MODIFIED REMARK 280 MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 57.57400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.04950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.57400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.04950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS REMARK 300 UNKNOWN. 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: MONOMERIC 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 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 GLY A 2 REMARK 465 VAL A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 VAL A 6 REMARK 465 PRO A 7 REMARK 465 LYS A 8 REMARK 465 TYR A 9 REMARK 465 ASP A 10 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 14 CE NZ REMARK 470 GLU A 17 CD OE1 OE2 REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 GLU A 115 CG CD OE1 OE2 REMARK 470 GLU A 128 CG CD OE1 OE2 REMARK 470 LYS A 129 CE NZ REMARK 470 GLU A 146 CD OE1 OE2 REMARK 470 LYS A 147 CD CE NZ REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 190 CG CD OE1 OE2 REMARK 470 GLU A 193 CD OE1 OE2 REMARK 470 GLU A 210 CD OE1 OE2 REMARK 470 LYS A 213 NZ REMARK 470 LYS A 237 CD CE NZ REMARK 470 GLU A 239 CD OE1 OE2 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 ASP A 63 CB - CG - OD2 ANGL. DEV. = 6.2 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 TYR A 100 -163.56 -128.46 REMARK 500 ASP A 127 111.90 -161.87 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 PEG A 303 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 NA A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 30 OE2 REMARK 620 2 GLU A 30 OE1 45.2 REMARK 620 3 THR A 223 O 130.1 98.8 REMARK 620 4 THR A 223 OG1 111.7 74.4 78.2 REMARK 620 5 HOH A 331 O 93.8 120.2 135.7 92.2 REMARK 620 6 HOH A 396 O 104.9 136.3 77.4 143.4 86.7 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 PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PFU-392566-001 RELATED DB: TARGETDB DBREF 1VK1 A 1 242 UNP Q8U3S5 Q8U3S5_PYRFU 1 242 SEQADV 1VK1 MLY A 27 UNP Q8U3S5 LYS 27 MODIFIED RESIDUE SEQADV 1VK1 MLY A 107 UNP Q8U3S5 LYS 107 MODIFIED RESIDUE SEQADV 1VK1 MLY A 112 UNP Q8U3S5 LYS 112 MODIFIED RESIDUE SEQADV 1VK1 MLY A 133 UNP Q8U3S5 LYS 133 MODIFIED RESIDUE SEQADV 1VK1 MLY A 136 UNP Q8U3S5 LYS 136 MODIFIED RESIDUE SEQADV 1VK1 MLY A 159 UNP Q8U3S5 LYS 159 MODIFIED RESIDUE SEQADV 1VK1 MLY A 172 UNP Q8U3S5 LYS 172 MODIFIED RESIDUE SEQADV 1VK1 MLY A 201 UNP Q8U3S5 LYS 201 MODIFIED RESIDUE SEQADV 1VK1 MLY A 221 UNP Q8U3S5 LYS 221 MODIFIED RESIDUE SEQRES 1 A 242 MET GLY VAL GLU LYS VAL PRO LYS TYR ASP ILE PRO VAL SEQRES 2 A 242 LYS LYS VAL GLU TYR VAL PHE ILE GLU LEU ASP LYS MET SEQRES 3 A 242 MLY PRO HIS GLU GLN LEU VAL GLN ARG GLU LEU GLU ASP SEQRES 4 A 242 PHE ILE GLU SER VAL THR GLY SER GLY ILE PHE TRP LYS SEQRES 5 A 242 PRO MET LEU LEU ALA LYS ILE PRO GLY THR ASP GLU TYR SEQRES 6 A 242 LEU ILE VAL ASP GLY HIS HIS ARG TRP ALA GLY LEU GLN SEQRES 7 A 242 LYS LEU GLY ALA LYS ARG ALA PRO SER VAL ILE LEU ASP SEQRES 8 A 242 TYR PHE ASP GLU GLY VAL LYS VAL TYR THR TRP TYR PRO SEQRES 9 A 242 ALA PHE MLY GLY ASP VAL ASN MLY VAL ILE GLU ARG LEU SEQRES 10 A 242 LYS ALA GLU GLY LEU GLU VAL ILE GLU ASP GLU LYS ALA SEQRES 11 A 242 GLU GLU MLY ALA GLU MLY GLY GLU ILE ALA PHE ALA LEU SEQRES 12 A 242 ILE GLY GLU LYS SER PHE ALA ILE PRO GLY GLY LEU GLU SEQRES 13 A 242 GLU GLN MLY LYS VAL SER LYS VAL LEU ASP GLU MET ASP SEQRES 14 A 242 GLN ALA MLY GLU ILE GLU LEU VAL TYR TYR GLY LEU LYS SEQRES 15 A 242 GLU ASP ALA LYS ALA ASP MET GLU LYS GLY GLU ILE ASP SEQRES 16 A 242 TYR VAL PHE ILE ARG MLY ALA PRO THR LYS GLU GLU VAL SEQRES 17 A 242 MET GLU LEU VAL LYS ARG GLY GLU VAL PHE SER PRO MLY SEQRES 18 A 242 THR THR ARG HIS VAL LEU PRO PHE ILE PRO ASP LYS ILE SEQRES 19 A 242 ASP VAL LYS LEU GLU ASP LEU PHE MODRES 1VK1 MLY A 27 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 107 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 112 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 133 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 136 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 159 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 172 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 201 LYS N-DIMETHYL-LYSINE MODRES 1VK1 MLY A 221 LYS N-DIMETHYL-LYSINE HET MLY A 27 11 HET MLY A 107 11 HET MLY A 112 11 HET MLY A 133 11 HET MLY A 136 11 HET MLY A 159 11 HET MLY A 172 11 HET MLY A 201 11 HET MLY A 221 18 HET PO4 A 301 5 HET NA A 302 1 HET PEG A 303 6 HETNAM MLY N-DIMETHYL-LYSINE HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 1 MLY 9(C8 H18 N2 O2) FORMUL 2 PO4 O4 P 3- FORMUL 3 NA NA 1+ FORMUL 4 PEG C4 H10 O3 FORMUL 5 HOH *137(H2 O) HELIX 1 1 VAL A 33 GLY A 48 1 16 HELIX 2 2 GLY A 70 GLY A 81 1 12 HELIX 3 3 ASP A 109 GLU A 120 1 12 HELIX 4 4 LYS A 129 MLY A 136 1 8 HELIX 5 5 GLY A 154 ALA A 171 1 18 HELIX 6 6 LEU A 181 LYS A 191 1 11 HELIX 7 7 THR A 204 ARG A 214 1 11 HELIX 8 8 GLU A 239 PHE A 242 5 4 SHEET 1 A 2 VAL A 13 LYS A 14 0 SHEET 2 A 2 ILE A 230 PRO A 231 1 O ILE A 230 N LYS A 14 SHEET 1 B 5 VAL A 19 GLU A 22 0 SHEET 2 B 5 ARG A 84 LEU A 90 -1 O SER A 87 N VAL A 19 SHEET 3 B 5 MET A 54 LYS A 58 1 N LEU A 56 O LEU A 90 SHEET 4 B 5 TYR A 65 ASP A 69 -1 O LEU A 66 N ALA A 57 SHEET 5 B 5 MET A 26 MLY A 27 1 N MLY A 27 O TYR A 65 SHEET 1 C 2 ILE A 49 PHE A 50 0 SHEET 2 C 2 VAL A 236 LYS A 237 -1 O VAL A 236 N PHE A 50 SHEET 1 D 2 LYS A 98 TYR A 100 0 SHEET 2 D 2 ARG A 224 VAL A 226 -1 O VAL A 226 N LYS A 98 SHEET 1 E 6 ILE A 125 GLU A 126 0 SHEET 2 E 6 SER A 148 ILE A 151 -1 O ALA A 150 N ILE A 125 SHEET 3 E 6 PHE A 141 ILE A 144 -1 N LEU A 143 O PHE A 149 SHEET 4 E 6 TYR A 196 ILE A 199 -1 O VAL A 197 N ILE A 144 SHEET 5 E 6 TYR A 103 MLY A 107 -1 N PRO A 104 O PHE A 198 SHEET 6 E 6 GLU A 175 TYR A 179 -1 O VAL A 177 N ALA A 105 LINK C MET A 26 N MLY A 27 1555 1555 1.32 LINK C MLY A 27 N PRO A 28 1555 1555 1.33 LINK C PHE A 106 N MLY A 107 1555 1555 1.34 LINK C MLY A 107 N GLY A 108 1555 1555 1.33 LINK C ASN A 111 N MLY A 112 1555 1555 1.32 LINK C MLY A 112 N VAL A 113 1555 1555 1.33 LINK C GLU A 132 N MLY A 133 1555 1555 1.33 LINK C MLY A 133 N ALA A 134 1555 1555 1.32 LINK C GLU A 135 N MLY A 136 1555 1555 1.33 LINK C MLY A 136 N GLY A 137 1555 1555 1.33 LINK C GLN A 158 N MLY A 159 1555 1555 1.33 LINK C MLY A 159 N LYS A 160 1555 1555 1.32 LINK C ALA A 171 N MLY A 172 1555 1555 1.33 LINK C MLY A 172 N GLU A 173 1555 1555 1.34 LINK C ARG A 200 N MLY A 201 1555 1555 1.32 LINK C MLY A 201 N ALA A 202 1555 1555 1.32 LINK C PRO A 220 N MLY A 221 1555 1555 1.31 LINK C MLY A 221 N THR A 222 1555 1555 1.32 LINK OE2 GLU A 30 NA NA A 302 1555 1555 2.28 LINK OE1 GLU A 30 NA NA A 302 1555 1555 3.04 LINK O THR A 223 NA NA A 302 1555 1555 2.28 LINK OG1 THR A 223 NA NA A 302 1555 1555 2.42 LINK NA NA A 302 O HOH A 331 1555 1555 2.20 LINK NA NA A 302 O HOH A 396 1555 1555 2.49 SITE 1 AC1 10 GLU A 30 GLY A 70 HIS A 71 HIS A 72 SITE 2 AC1 10 MLY A 221 HOH A 307 HOH A 319 HOH A 331 SITE 3 AC1 10 HOH A 348 HOH A 396 SITE 1 AC2 4 GLU A 30 THR A 223 HOH A 331 HOH A 396 SITE 1 AC3 7 GLN A 158 ARG A 200 MLY A 201 PRO A 203 SITE 2 AC3 7 GLU A 207 HOH A 434 HOH A 435 CRYST1 115.148 40.099 65.671 90.00 122.29 90.00 C 1 2 1 4 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 0.008684 0.000000 0.005488 0.00000 SCALE2 0.000000 0.024938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018013 0.00000