HEADER HYDROLASE/TRANSFERASE 07-DEC-05 2FAQ
TITLE CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LIGD POLYMERASE DOMAIN
TITLE 2 WITH ATP AND MANGANESE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT DNA LIGASE;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: POLYMERASE DOMAIN, RESIDUES 533-840;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA;
SOURCE 3 ORGANISM_TAXID: 287;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834 DE3;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSMT3, PET28B DERIVED
KEYWDS POLYMERASE, PRIMASE, LIGASE, NHEJ, ATP, HYDROLASE-TRANSFERASE COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR H.ZHU,J.NANDAKUMAR,J.ANIUKWU,L.K.WANG,M.S.GLICKMAN,C.D.LIMA,S.SHUMAN
REVDAT 3 18-OCT-17 2FAQ 1 REMARK
REVDAT 2 24-FEB-09 2FAQ 1 VERSN
REVDAT 1 23-MAY-06 2FAQ 0
JRNL AUTH H.ZHU,J.NANDAKUMAR,J.ANIUKWU,L.K.WANG,M.S.GLICKMAN,C.D.LIMA,
JRNL AUTH 2 S.SHUMAN
JRNL TITL ATOMIC STRUCTURE AND NONHOMOLOGOUS END-JOINING FUNCTION OF
JRNL TITL 2 THE POLYMERASE COMPONENT OF BACTERIAL DNA LIGASE D
JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 1711 2006
JRNL REFN ISSN 0027-8424
JRNL PMID 16446439
JRNL DOI 10.1073/PNAS.0509083103
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.57
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2176385.370
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6
REMARK 3 NUMBER OF REFLECTIONS : 97202
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) : 0.198
REMARK 3 FREE R VALUE : 0.226
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 4821
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.70
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 14607
REMARK 3 BIN R VALUE (WORKING SET) : 0.1950
REMARK 3 BIN FREE R VALUE : 0.2400
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 774
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4642
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 81
REMARK 3 SOLVENT ATOMS : 462
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 8.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.96000
REMARK 3 B22 (A**2) : 0.96000
REMARK 3 B33 (A**2) : 0.00000
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) : 0.21
REMARK 3 ESD FROM SIGMAA (A) : 0.03
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.200
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.140 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.680 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.170 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.080 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.39
REMARK 3 BSOL : 40.80
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 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : ION.PARAM
REMARK 3 PARAMETER FILE 4 : ATP.PAR
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : ION.TOP
REMARK 3 TOPOLOGY FILE 4 : ATP.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2FAQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-05.
REMARK 100 THE DEPOSITION ID IS D_1000035659.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-JUN-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X29A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL
REMARK 200 SAGITTAL FOCUSING MONOCHROMETER
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97263
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 41.570
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.05400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.09800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 22.80
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NATIVE MODEL
REMARK 200 STARTING MODEL: PDB ENTRY 2FAO
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.87
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE, 0.2 M SODIUM
REMARK 280 ACETATE, 5 MM DTT,26-32% POLYETHYLENE GLYCOL-8000, 10 MM
REMARK 280 MANGANOUS CHLORIDE, 5 MM ATP, PH 6.5, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+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 35.81600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 102.09850
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.81600
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 102.09850
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 532
REMARK 465 GLY A 533
REMARK 465 ALA A 534
REMARK 465 ARG A 535
REMARK 465 LYS A 536
REMARK 465 ALA A 537
REMARK 465 SER A 538
REMARK 465 ALA A 539
REMARK 465 GLY A 540
REMARK 465 ALA A 541
REMARK 465 SER A 542
REMARK 465 GLY A 838
REMARK 465 ARG A 839
REMARK 465 GLY A 840
REMARK 465 MET B 532
REMARK 465 GLY B 533
REMARK 465 ALA B 534
REMARK 465 ARG B 535
REMARK 465 LYS B 536
REMARK 465 ALA B 537
REMARK 465 SER B 538
REMARK 465 ALA B 539
REMARK 465 GLY B 540
REMARK 465 ALA B 541
REMARK 465 SER B 542
REMARK 465 GLY B 838
REMARK 465 ARG B 839
REMARK 465 GLY B 840
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 PRO A 614 107.64 -54.14
REMARK 500 ASP A 624 74.24 -155.96
REMARK 500 ASN A 659 98.43 -165.39
REMARK 500 PRO A 674 0.76 -57.51
REMARK 500 ARG A 752 33.94 -149.64
REMARK 500 HIS B 553 56.86 39.79
REMARK 500 PRO B 614 85.45 -57.85
REMARK 500 ASP B 624 72.33 -160.08
REMARK 500 ASN B 654 33.31 -90.98
REMARK 500 ASN B 659 103.95 -169.01
REMARK 500 ARG B 665 166.49 177.17
REMARK 500 ARG B 752 31.19 -147.10
REMARK 500 ASN B 763 50.81 -105.94
REMARK 500
REMARK 500 REMARK: NULL
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 MN A 501 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 669 OD1
REMARK 620 2 ASP A 669 OD2 52.1
REMARK 620 3 HOH A 155 O 62.9 114.5
REMARK 620 4 HOH A 278 O 121.7 70.7 173.9
REMARK 620 5 ASP A 671 OD1 115.6 102.8 97.8 83.9
REMARK 620 6 ATP A1304 O1G 148.1 154.3 89.5 84.9 81.8
REMARK 620 7 ATP A1304 O1B 83.0 92.9 85.7 90.8 160.7 79.2
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 502 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 669 OD2
REMARK 620 2 ASP A 671 OD2 67.3
REMARK 620 3 HOH A 278 O 65.9 81.7
REMARK 620 4 ASP A 759 OD2 119.5 96.6 173.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN B 503 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ATP B1302 O1G
REMARK 620 2 ATP B1302 O1B 78.6
REMARK 620 3 HOH B 415 O 91.8 79.8
REMARK 620 4 ASP B 669 OD1 160.5 97.5 68.7
REMARK 620 5 ASP B 669 OD2 139.8 67.9 103.0 50.7
REMARK 620 6 HOH B 431 O 89.9 96.5 175.5 109.5 73.0
REMARK 620 7 ASP B 671 OD1 79.1 157.7 99.7 103.1 132.8 84.7
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN B 504 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 671 OD2
REMARK 620 2 ASP B 759 OD2 104.1
REMARK 620 3 HOH B 431 O 75.9 176.5
REMARK 620 4 HOH B 300 O 66.5 64.1 113.0
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 1302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1304
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2FAO RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LIGD POLYMERASE DOMAIN
REMARK 900 RELATED ID: 2FAR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LIGD POLYMERASE DOMAIN
REMARK 900 WITH DATP AND MANGANESE
DBREF 2FAQ A 533 840 UNP Q9I1X7 Q9I1X7_PSEAE 533 840
DBREF 2FAQ B 533 840 UNP Q9I1X7 Q9I1X7_PSEAE 533 840
SEQADV 2FAQ MET A 532 UNP Q9I1X7 INITIATING METHIONINE
SEQADV 2FAQ MET B 532 UNP Q9I1X7 INITIATING METHIONINE
SEQRES 1 A 309 MET GLY ALA ARG LYS ALA SER ALA GLY ALA SER ARG ALA
SEQRES 2 A 309 ALA THR ALA GLY VAL ARG ILE SER HIS PRO GLN ARG LEU
SEQRES 3 A 309 ILE ASP PRO SER ILE GLN ALA SER LYS LEU GLU LEU ALA
SEQRES 4 A 309 GLU PHE HIS ALA ARG TYR ALA ASP LEU LEU LEU ARG ASP
SEQRES 5 A 309 LEU ARG GLU ARG PRO VAL SER LEU VAL ARG GLY PRO ASP
SEQRES 6 A 309 GLY ILE GLY GLY GLU LEU PHE PHE GLN LYS HIS ALA ALA
SEQRES 7 A 309 ARG LEU LYS ILE PRO GLY ILE VAL GLN LEU ASP PRO ALA
SEQRES 8 A 309 LEU ASP PRO GLY HIS PRO PRO LEU LEU GLN ILE ARG SER
SEQRES 9 A 309 ALA GLU ALA LEU VAL GLY ALA VAL GLN MET GLY SER ILE
SEQRES 10 A 309 GLU PHE HIS THR TRP ASN ALA SER LEU ALA ASN LEU GLU
SEQRES 11 A 309 ARG PRO ASP ARG PHE VAL LEU ASP LEU ASP PRO ASP PRO
SEQRES 12 A 309 ALA LEU PRO TRP LYS ARG MET LEU GLU ALA THR GLN LEU
SEQRES 13 A 309 SER LEU THR LEU LEU ASP GLU LEU GLY LEU ARG ALA PHE
SEQRES 14 A 309 LEU LYS THR SER GLY GLY LYS GLY MET HIS LEU LEU VAL
SEQRES 15 A 309 PRO LEU GLU ARG ARG HIS GLY TRP ASP GLU VAL LYS ASP
SEQRES 16 A 309 PHE ALA GLN ALA ILE SER GLN HIS LEU ALA ARG LEU MET
SEQRES 17 A 309 PRO GLU ARG PHE SER ALA VAL SER GLY PRO ARG ASN ARG
SEQRES 18 A 309 VAL GLY LYS ILE PHE VAL ASP TYR LEU ARG ASN SER ARG
SEQRES 19 A 309 GLY ALA SER THR VAL ALA ALA TYR SER VAL ARG ALA ARG
SEQRES 20 A 309 GLU GLY LEU PRO VAL SER VAL PRO VAL PHE ARG GLU GLU
SEQRES 21 A 309 LEU ASP SER LEU GLN GLY ALA ASN GLN TRP ASN LEU ARG
SEQRES 22 A 309 SER LEU PRO GLN ARG LEU ASP GLU LEU ALA GLY ASP ASP
SEQRES 23 A 309 PRO TRP ALA ASP TYR ALA GLY THR ARG GLN ARG ILE SER
SEQRES 24 A 309 ALA ALA MET ARG ARG GLN LEU GLY ARG GLY
SEQRES 1 B 309 MET GLY ALA ARG LYS ALA SER ALA GLY ALA SER ARG ALA
SEQRES 2 B 309 ALA THR ALA GLY VAL ARG ILE SER HIS PRO GLN ARG LEU
SEQRES 3 B 309 ILE ASP PRO SER ILE GLN ALA SER LYS LEU GLU LEU ALA
SEQRES 4 B 309 GLU PHE HIS ALA ARG TYR ALA ASP LEU LEU LEU ARG ASP
SEQRES 5 B 309 LEU ARG GLU ARG PRO VAL SER LEU VAL ARG GLY PRO ASP
SEQRES 6 B 309 GLY ILE GLY GLY GLU LEU PHE PHE GLN LYS HIS ALA ALA
SEQRES 7 B 309 ARG LEU LYS ILE PRO GLY ILE VAL GLN LEU ASP PRO ALA
SEQRES 8 B 309 LEU ASP PRO GLY HIS PRO PRO LEU LEU GLN ILE ARG SER
SEQRES 9 B 309 ALA GLU ALA LEU VAL GLY ALA VAL GLN MET GLY SER ILE
SEQRES 10 B 309 GLU PHE HIS THR TRP ASN ALA SER LEU ALA ASN LEU GLU
SEQRES 11 B 309 ARG PRO ASP ARG PHE VAL LEU ASP LEU ASP PRO ASP PRO
SEQRES 12 B 309 ALA LEU PRO TRP LYS ARG MET LEU GLU ALA THR GLN LEU
SEQRES 13 B 309 SER LEU THR LEU LEU ASP GLU LEU GLY LEU ARG ALA PHE
SEQRES 14 B 309 LEU LYS THR SER GLY GLY LYS GLY MET HIS LEU LEU VAL
SEQRES 15 B 309 PRO LEU GLU ARG ARG HIS GLY TRP ASP GLU VAL LYS ASP
SEQRES 16 B 309 PHE ALA GLN ALA ILE SER GLN HIS LEU ALA ARG LEU MET
SEQRES 17 B 309 PRO GLU ARG PHE SER ALA VAL SER GLY PRO ARG ASN ARG
SEQRES 18 B 309 VAL GLY LYS ILE PHE VAL ASP TYR LEU ARG ASN SER ARG
SEQRES 19 B 309 GLY ALA SER THR VAL ALA ALA TYR SER VAL ARG ALA ARG
SEQRES 20 B 309 GLU GLY LEU PRO VAL SER VAL PRO VAL PHE ARG GLU GLU
SEQRES 21 B 309 LEU ASP SER LEU GLN GLY ALA ASN GLN TRP ASN LEU ARG
SEQRES 22 B 309 SER LEU PRO GLN ARG LEU ASP GLU LEU ALA GLY ASP ASP
SEQRES 23 B 309 PRO TRP ALA ASP TYR ALA GLY THR ARG GLN ARG ILE SER
SEQRES 24 B 309 ALA ALA MET ARG ARG GLN LEU GLY ARG GLY
HET MN A 501 1
HET MN A 502 1
HET SO4 A1302 5
HET SO4 A1303 5
HET ATP A1304 31
HET MN B 503 1
HET MN B 504 1
HET SO4 B1301 5
HET ATP B1302 31
HETNAM MN MANGANESE (II) ION
HETNAM SO4 SULFATE ION
HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE
FORMUL 3 MN 4(MN 2+)
FORMUL 5 SO4 3(O4 S 2-)
FORMUL 7 ATP 2(C10 H16 N5 O13 P3)
FORMUL 12 HOH *462(H2 O)
HELIX 1 1 LYS A 566 TYR A 576 1 11
HELIX 2 2 TYR A 576 ARG A 585 1 10
HELIX 3 3 ASP A 620 ASP A 624 5 5
HELIX 4 4 SER A 635 MET A 645 1 11
HELIX 5 5 PRO A 677 GLY A 696 1 20
HELIX 6 6 GLY A 720 MET A 739 1 20
HELIX 7 7 GLY A 748 ARG A 752 5 5
HELIX 8 8 TYR A 760 SER A 764 5 5
HELIX 9 9 PHE A 788 LEU A 795 5 8
HELIX 10 10 SER A 805 ALA A 814 1 10
HELIX 11 11 SER A 830 LEU A 837 1 8
HELIX 12 12 ARG B 543 ALA B 547 5 5
HELIX 13 13 PRO B 560 GLN B 563 5 4
HELIX 14 14 LYS B 566 TYR B 576 1 11
HELIX 15 15 TYR B 576 ARG B 585 1 10
HELIX 16 16 ASP B 620 ASP B 624 5 5
HELIX 17 17 SER B 635 MET B 645 1 11
HELIX 18 18 PRO B 677 GLY B 696 1 20
HELIX 19 19 GLY B 720 MET B 739 1 20
HELIX 20 20 GLY B 748 ARG B 752 5 5
HELIX 21 21 PHE B 788 LEU B 795 5 8
HELIX 22 22 SER B 805 ALA B 814 1 10
HELIX 23 23 SER B 830 LEU B 837 1 8
SHEET 1 A 2 LEU A 557 ASP A 559 0
SHEET 2 A 2 ALA A 564 SER A 565 -1 O ALA A 564 N ILE A 558
SHEET 1 B 4 PHE A 603 GLN A 605 0
SHEET 2 B 4 VAL A 589 ARG A 593 -1 N ARG A 593 O PHE A 603
SHEET 3 B 4 SER A 647 THR A 652 -1 O HIS A 651 N SER A 590
SHEET 4 B 4 THR A 769 VAL A 770 -1 O THR A 769 N THR A 652
SHEET 1 C 2 VAL A 617 GLN A 618 0
SHEET 2 C 2 LEU A 631 GLN A 632 -1 O GLN A 632 N VAL A 617
SHEET 1 D 6 PHE A 743 SER A 744 0
SHEET 2 D 6 ILE A 756 ASP A 759 1 O VAL A 758 N SER A 744
SHEET 3 D 6 ARG A 665 PRO A 672 -1 N ASP A 671 O PHE A 757
SHEET 4 D 6 MET A 709 PRO A 714 -1 O LEU A 711 N LEU A 668
SHEET 5 D 6 PHE A 700 THR A 703 -1 N PHE A 700 O LEU A 712
SHEET 6 D 6 PRO A 786 VAL A 787 -1 O VAL A 787 N LEU A 701
SHEET 1 E 2 LEU B 557 ASP B 559 0
SHEET 2 E 2 ALA B 564 SER B 565 -1 O ALA B 564 N ILE B 558
SHEET 1 F 4 PHE B 603 GLN B 605 0
SHEET 2 F 4 VAL B 589 ARG B 593 -1 N ARG B 593 O PHE B 603
SHEET 3 F 4 SER B 647 THR B 652 -1 O HIS B 651 N SER B 590
SHEET 4 F 4 THR B 769 VAL B 770 -1 O THR B 769 N THR B 652
SHEET 1 G 2 VAL B 617 GLN B 618 0
SHEET 2 G 2 LEU B 631 GLN B 632 -1 O GLN B 632 N VAL B 617
SHEET 1 H 6 PHE B 743 SER B 744 0
SHEET 2 H 6 ILE B 756 ASP B 759 1 O ILE B 756 N SER B 744
SHEET 3 H 6 ARG B 665 PRO B 672 -1 N ASP B 669 O ASP B 759
SHEET 4 H 6 MET B 709 PRO B 714 -1 O LEU B 711 N LEU B 668
SHEET 5 H 6 PHE B 700 THR B 703 -1 N LYS B 702 O HIS B 710
SHEET 6 H 6 PRO B 786 VAL B 787 -1 O VAL B 787 N LEU B 701
LINK MN MN A 501 OD1 ASP A 669 1555 1555 2.59
LINK MN MN A 501 OD2 ASP A 669 1555 1555 2.37
LINK MN MN A 501 O HOH A 155 1555 1555 2.32
LINK MN MN A 501 O HOH A 278 1555 1555 2.40
LINK MN MN A 501 OD1 ASP A 671 1555 1555 2.35
LINK MN MN A 501 O1G ATP A1304 1555 1555 2.27
LINK MN MN A 501 O1B ATP A1304 1555 1555 2.32
LINK MN MN A 502 OD2 ASP A 669 1555 1555 2.67
LINK MN MN A 502 OD2 ASP A 671 1555 1555 2.51
LINK MN MN A 502 O HOH A 278 1555 1555 2.39
LINK MN MN A 502 OD2 ASP A 759 1555 1555 2.35
LINK MN MN B 503 O1G ATP B1302 1555 1555 2.31
LINK MN MN B 503 O1B ATP B1302 1555 1555 2.26
LINK MN MN B 503 O HOH B 415 1555 1555 2.35
LINK MN MN B 503 OD1 ASP B 669 1555 1555 2.38
LINK MN MN B 503 OD2 ASP B 669 1555 1555 2.69
LINK MN MN B 503 O HOH B 431 1555 1555 2.19
LINK MN MN B 503 OD1 ASP B 671 1555 1555 2.28
LINK MN MN B 504 OD2 ASP B 671 1555 1555 2.54
LINK MN MN B 504 OD2 ASP B 759 1555 1555 2.45
LINK MN MN B 504 O HOH B 431 1555 1555 2.28
LINK MN MN B 504 O HOH B 300 1555 1555 2.61
SITE 1 AC1 5 HOH A 155 HOH A 278 ASP A 669 ASP A 671
SITE 2 AC1 5 ATP A1304
SITE 1 AC2 5 HOH A 278 ASP A 669 ASP A 671 ASP A 759
SITE 2 AC2 5 ARG A 762
SITE 1 AC3 5 HOH B 415 HOH B 431 ASP B 669 ASP B 671
SITE 2 AC3 5 ATP B1302
SITE 1 AC4 6 HOH B 300 HOH B 431 ASP B 669 ASP B 671
SITE 2 AC4 6 ASP B 759 ARG B 762
SITE 1 AC5 7 HOH A 162 HOH B 175 HOH B 330 SER B 552
SITE 2 AC5 7 HIS B 553 ARG B 556 LYS B 566
SITE 1 AC6 5 HOH A 84 SER A 552 HIS A 553 ARG A 556
SITE 2 AC6 5 LYS A 566
SITE 1 AC7 6 HOH A 212 HOH A 245 ARG A 750 ASN A 751
SITE 2 AC7 6 ARG B 750 ASN B 751
SITE 1 AC8 24 HOH B 71 HOH B 77 HOH B 94 HOH B 157
SITE 2 AC8 24 HOH B 231 HOH B 273 HOH B 370 HOH B 404
SITE 3 AC8 24 HOH B 415 HOH B 431 MN B 503 PHE B 604
SITE 4 AC8 24 HIS B 651 ASP B 669 ASP B 671 SER B 704
SITE 5 AC8 24 LYS B 707 GLY B 708 HIS B 710 ARG B 762
SITE 6 AC8 24 SER B 768 THR B 769 ARG B 776 ARG B 778
SITE 1 AC9 21 HOH A 32 HOH A 47 HOH A 130 HOH A 145
SITE 2 AC9 21 HOH A 155 HOH A 204 HOH A 278 HOH A 395
SITE 3 AC9 21 MN A 501 PHE A 604 HIS A 651 ASP A 669
SITE 4 AC9 21 ASP A 671 SER A 704 LYS A 707 GLY A 708
SITE 5 AC9 21 HIS A 710 ARG A 762 SER A 768 ARG A 776
SITE 6 AC9 21 ARG A 778
CRYST1 71.632 204.197 44.152 90.00 90.00 90.00 P 21 21 2 8
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 0.013960 0.000000 0.000000 0.00000
SCALE2 0.000000 0.004897 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022649 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
