10 20 30 40 50 60 70 80 4BDP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA 17-NOV-97 4BDP
TITLE CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT TITLE 2 COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TITLE 3 TWO DATP RESIDUES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3'); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3'); COMPND 8 CHAIN: T; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PROTEIN (DNA POLYMERASE I); COMPND 12 CHAIN: A; COMPND 13 FRAGMENT: RESIDUES 297-876; COMPND 14 SYNONYM: BF; COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 7 ORGANISM_TAXID: 1422; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS BACILLUS STEAROTHERMOPHILUS DNA POLYMERASE, BF THERMOPHILUS KEYWDS 2 POLYMERASE, COMPLEX (NUCLEOTIDYLTRANSFERASE/DNA)
EXPDTA X-RAY DIFFRACTION
AUTHOR J.R.KIEFER,C.MAO,L.S.BEESE
REVDAT 2 24-FEB-09 4BDP 1 VERSN REVDAT 1 13-JAN-99 4BDP 0
JRNL AUTH J.R.KIEFER,C.MAO,J.C.BRAMAN,L.S.BEESE JRNL TITL VISUALIZING DNA REPLICATION IN A CATALYTICALLY JRNL TITL 2 ACTIVE BACILLUS DNA POLYMERASE CRYSTAL. JRNL REF NATURE V. 391 304 1998 JRNL REFN ISSN 0028-0836 JRNL PMID 9440698 JRNL DOI 10.1038/34693
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.KIEFER,C.MAO,C.J.HANSEN,S.L.BASEHORE, REMARK 1 AUTH 2 H.H.HOGREFE,J.C.BRAMAN,L.S.BEESE REMARK 1 TITL CRYSTAL STRUCTURE OF A THERMOSTABLE BACILLUS DNA REMARK 1 TITL 2 POLYMERASE I LARGE FRAGMENT AT 2.1 A RESOLUTION REMARK 1 REF STRUCTURE V. 5 95 1997 REMARK 1 REFN ISSN 0969-2126
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.9 REMARK 3 NUMBER OF REFLECTIONS : 72346 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 SET) : 0.248 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3680 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9491 REMARK 3 BIN R VALUE (WORKING SET) : 0.4210 REMARK 3 BIN FREE R VALUE : 0.4220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 520 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4650 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 554 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.16000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.94 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.750 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.280 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.390 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.270 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : DNA-RNA-MULTI-ENDO.PARAM REMARK 3 PARAMETER FILE 4 : PARAM_SULFATE.TXT REMARK 3 PARAMETER FILE 5 : PARAMETER.ELEMENTS REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : DNA-RNA-MULTI-ENDO.TOP REMARK 3 TOPOLOGY FILE 4 : TOP_SULFATE.TXT REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 4BDP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-97 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72444 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13300 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 2BDP REMARK 200 REMARK 200 REMARK: LTI/SIGMA(I)> FOR THE DATA SET : 18.9 LTI/SIGMA(I)> FOR REMARK 200 SHELL : 5.6
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.8
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 43.12050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.18700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.63750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.18700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.12050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.63750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, 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 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 ARG A 411 CG CD NE CZ NH1 NH2
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 2054 O HOH A 2350 2.06 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 LEU A 834 CA - CB - CG ANGL. DEV. = 19.4 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 ASP A 402 93.84 -167.78 REMARK 500 ALA A 421 37.85 -83.88 REMARK 500 ALA A 436 148.53 169.09 REMARK 500 GLN A 524 174.63 174.31 REMARK 500 ILE A 528 -15.81 -47.43 REMARK 500 PRO A 531 -22.96 -32.50 REMARK 500 LYS A 551 31.50 -65.39 REMARK 500 THR A 552 -8.19 -176.91 REMARK 500 ILE A 588 -61.78 -107.70 REMARK 500 LEU A 610 -52.20 -131.32 REMARK 500 ASN A 625 35.52 -140.32 REMARK 500 ILE A 628 -35.42 -159.55 REMARK 500 HIS A 829 -52.31 65.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA T 3 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH T2275 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A2607 DISTANCE = 5.40 ANGSTROMS
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 950 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 653 OD2 REMARK 620 2 ASP A 830 OD2 126.9 REMARK 620 3 TYR A 654 O 78.6 78.5 REMARK 620 4 HOH A2511 O 121.0 96.4 72.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 952 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2516 O REMARK 620 2 SO4 A 911 O1 168.4 REMARK 620 3 SO4 A 911 O3 126.2 54.6 REMARK 620 N 1 2
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 910 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 911 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 912 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 950 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 952
DBREF 4BDP A 297 876 UNP P52026 DPO1_BACST 297 877 DBREF 4BDP P 19 29 PDB 4BDP 4BDP 19 29 DBREF 4BDP T 2 14 PDB 4BDP 4BDP 2 14
SEQADV 4BDP ALA A 298 UNP P52026 LYS 298 CONFLICT SEQADV 4BDP ARG A 411 UNP P52026 ALA 411 CONFLICT SEQADV 4BDP GLU A 456 UNP P52026 ALA 456 CONFLICT SEQADV 4BDP LYS A 505 UNP P52026 GLU 505 CONFLICT SEQADV 4BDP GLY A 512 UNP P52026 ARG 512 CONFLICT SEQADV 4BDP THR A 550 UNP P52026 SER 550 CONFLICT SEQADV 4BDP A UNP P52026 GLN 576 DELETION SEQADV 4BDP HIS A 823 UNP P52026 ARG 824 CONFLICT
SEQRES 1 P 11 DG DC DA DT DC DA DT DG DC DA DA SEQRES 1 T 13 DT DA DT DT DG DC DA DT DG DA DT DG DC SEQRES 1 A 580 ALA ALA MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU SEQRES 2 A 580 GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL SEQRES 3 A 580 VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE SEQRES 4 A 580 ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO SEQRES 5 A 580 GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU SEQRES 6 A 580 GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS SEQRES 7 A 580 ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU SEQRES 8 A 580 CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU SEQRES 9 A 580 LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ARG ALA ALA SEQRES 10 A 580 ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU SEQRES 11 A 580 ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP SEQRES 12 A 580 GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA SEQRES 13 A 580 ALA ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU SEQRES 14 A 580 ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU SEQRES 15 A 580 GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA SEQRES 16 A 580 GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY SEQRES 17 A 580 LYS GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG SEQRES 18 A 580 ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER SEQRES 19 A 580 PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN SEQRES 20 A 580 LEU PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SEQRES 21 A 580 SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU SEQRES 22 A 580 ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS SEQRES 23 A 580 LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL SEQRES 24 A 580 ARG PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN GLN SEQRES 25 A 580 ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO SEQRES 26 A 580 ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG SEQRES 27 A 580 LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP SEQRES 28 A 580 LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG SEQRES 29 A 580 VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU SEQRES 30 A 580 ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA SEQRES 31 A 580 MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO SEQRES 32 A 580 ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY ILE SEQRES 33 A 580 VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU SEQRES 34 A 580 ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG SEQRES 35 A 580 TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU SEQRES 36 A 580 ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR SEQRES 37 A 580 THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SEQRES 38 A 580 SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET SEQRES 39 A 580 ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE SEQRES 40 A 580 ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS SEQRES 41 A 580 GLU GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS SEQRES 42 A 580 ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU SEQRES 43 A 580 ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA SEQRES 44 A 580 VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR SEQRES 45 A 580 GLY SER THR TRP TYR ASP ALA LYS
HET SO4 A 910 5 HET SO4 A 911 5 HET SO4 A 912 5 HET MG A 950 1 HET MG A 952 1
HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION
FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 MG 2(MG 2+) FORMUL 9 HOH *554(H2 O)
HELIX 1 1 GLU A 309 LEU A 312 5 4 HELIX 2 2 PRO A 348 ALA A 351 1 4 HELIX 3 3 PRO A 355 GLY A 362 1 8 HELIX 4 4 SER A 373 LYS A 383 1 11 HELIX 5 5 LEU A 394 LEU A 401 1 8 HELIX 6 6 PRO A 403 GLN A 405 5 3 HELIX 7 7 VAL A 410 LYS A 417 1 8 HELIX 8 8 ASP A 425 TYR A 429 1 5 HELIX 9 9 GLU A 440 ARG A 467 1 28 HELIX 10 10 ASP A 471 GLU A 476 1 6 HELIX 11 11 GLU A 478 ALA A 491 1 14 HELIX 12 12 THR A 497 ALA A 522 1 26 HELIX 13 13 PRO A 531 PHE A 539 1 9 HELIX 14 14 ALA A 558 TYR A 567 1 10 HELIX 15 15 GLU A 569 TYR A 587 1 19 HELIX 16 16 GLU A 589 VAL A 594 1 6 HELIX 17 17 GLU A 631 ALA A 639 1 9 HELIX 18 18 ILE A 657 ALA A 666 1 10 HELIX 19 19 ASP A 669 ARG A 676 1 8 HELIX 20 20 ILE A 681 ILE A 689 1 9 HELIX 21 21 GLU A 694 GLU A 696 5 3 HELIX 22 22 PRO A 699 TYR A 714 1 16 HELIX 23 23 ASP A 718 LEU A 725 1 8 HELIX 24 24 ARG A 729 SER A 742 1 14 HELIX 25 25 PRO A 744 LYS A 760 1 17 HELIX 26 26 PRO A 774 THR A 777 5 4 HELIX 27 27 PHE A 781 GLU A 817 1 37 HELIX 28 28 LYS A 838 GLN A 854 5 17 HELIX 29 29 TRP A 872 ASP A 874 5 3
SHEET 1 A 6 THR A 302 ALA A 304 0 SHEET 2 A 6 GLY A 342 LEU A 346 1 N PHE A 345 O THR A 302 SHEET 3 A 6 GLY A 334 ASN A 339 -1 N ASN A 339 O GLY A 342 SHEET 4 A 6 LYS A 315 GLU A 321 -1 N GLU A 321 O GLY A 334 SHEET 5 A 6 LYS A 367 MET A 370 1 N LYS A 367 O ALA A 316 SHEET 6 A 6 VAL A 390 ASP A 393 1 N SER A 391 O LYS A 368 SHEET 1 B 2 ILE A 605 ASN A 607 0 SHEET 2 B 2 SER A 617 THR A 619 -1 N THR A 619 O ILE A 605 SHEET 1 C 4 VAL A 864 GLY A 869 0 SHEET 2 C 4 TRP A 647 TYR A 654 -1 N ASP A 653 O ASP A 865 SHEET 3 C 4 GLU A 831 PRO A 837 -1 N ALA A 836 O LEU A 648 SHEET 4 C 4 HIS A 823 GLN A 827 -1 N LEU A 826 O ILE A 833 SHEET 1 D 2 TYR A 762 THR A 764 0 SHEET 2 D 2 ARG A 770 TYR A 772 -1 N ARG A 771 O VAL A 763
LINK MG MG A 950 OD2 ASP A 653 1555 1555 2.61 LINK MG MG A 950 OD2 ASP A 830 1555 1555 3.14 LINK MG MG A 950 O TYR A 654 1555 1555 2.72 LINK MG MG A 950 O HOH A2511 1555 1555 3.11 LINK MG MG A 952 O HOH A2516 1555 3545 2.84 LINK MG MG A 952 O1 SO4 A 911 1555 3545 3.14 LINK MG MG A 952 O3 SO4 A 911 1555 3545 2.54
CISPEP 1 GLU A 620 PRO A 621 0 -0.28
SITE 1 AC1 4 HIS A 682 ARG A 702 LYS A 706 HOH A2611 SITE 1 AC2 4 ARG A 779 ARG A 819 MG A 952 HOH A2590 SITE 1 AC3 4 MET A 299 ALA A 300 ARG A 343 ARG A 677 SITE 1 AC4 3 ASP A 653 TYR A 654 ASP A 830 SITE 1 AC5 3 GLU A 817 SO4 A 911 HOH A2516
CRYST1 86.241 93.275 106.374 90.00 90.00 90.00 P 21 21 21 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 0.011595 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010721 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009401 0.00000