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 4 30-AUG-23 2FAQ 1 REMARK SEQADV LINK 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 HOH A 155 O REMARK 620 2 HOH A 278 O 173.9 REMARK 620 3 ASP A 669 OD1 62.9 121.7 REMARK 620 4 ASP A 669 OD2 114.5 70.7 52.1 REMARK 620 5 ASP A 671 OD1 97.8 83.9 115.6 102.8 REMARK 620 6 ATP A1304 O1G 89.5 84.9 148.1 154.3 81.8 REMARK 620 7 ATP A1304 O1B 85.7 90.8 83.0 92.9 160.7 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 HOH A 278 O REMARK 620 2 ASP A 669 OD2 65.9 REMARK 620 3 ASP A 671 OD2 81.7 67.3 REMARK 620 4 ASP A 759 OD2 173.3 119.5 96.6 REMARK 620 N 1 2 3 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 HOH B 300 O REMARK 620 2 HOH B 431 O 113.0 REMARK 620 3 ASP B 671 OD2 66.5 75.9 REMARK 620 4 ASP B 759 OD2 64.1 176.5 104.1 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 HOH B 415 O REMARK 620 2 HOH B 431 O 175.5 REMARK 620 3 ASP B 669 OD1 68.7 109.5 REMARK 620 4 ASP B 669 OD2 103.0 73.0 50.7 REMARK 620 5 ASP B 671 OD1 99.7 84.7 103.1 132.8 REMARK 620 6 ATP B1302 O1G 91.8 89.9 160.5 139.8 79.1 REMARK 620 7 ATP B1302 O1B 79.8 96.5 97.5 67.9 157.7 78.6 REMARK 620 N 1 2 3 4 5 6 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 O HOH A 155 MN MN A 501 1555 1555 2.32 LINK O HOH A 278 MN MN A 501 1555 1555 2.40 LINK O HOH A 278 MN MN A 502 1555 1555 2.39 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 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 OD2 ASP A 759 1555 1555 2.35 LINK O HOH B 300 MN MN B 504 1555 1555 2.61 LINK O HOH B 415 MN MN B 503 1555 1555 2.35 LINK O HOH B 431 MN MN B 503 1555 1555 2.19 LINK O HOH B 431 MN MN B 504 1555 1555 2.28 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 OD1 ASP B 671 1555 1555 2.28 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 504 OD2 ASP B 671 1555 1555 2.54 LINK MN MN B 504 OD2 ASP B 759 1555 1555 2.45 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