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 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,VAGIN,DODSON 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 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 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 HOH A 331 O REMARK 620 2 THR A 223 O 135.7 REMARK 620 3 GLU A 30 OE2 93.8 130.1 REMARK 620 4 THR A 223 OG1 92.2 78.2 111.7 REMARK 620 5 HOH A 396 O 86.7 77.4 104.9 143.4 REMARK 620 6 GLU A 30 OE1 120.2 98.8 45.2 74.4 136.3 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 NA NA A 302 O HOH A 331 1555 1555 2.20 LINK NA NA A 302 O THR A 223 1555 1555 2.28 LINK NA NA A 302 OE2 GLU A 30 1555 1555 2.28 LINK NA NA A 302 OG1 THR A 223 1555 1555 2.42 LINK NA NA A 302 O HOH A 396 1555 1555 2.49 LINK OE1 GLU A 30 NA NA A 302 1555 1555 3.04 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 MASTER 358 0 12 8 17 0 6 6 0 0 0 19 END