HEADER LIGASE 29-APR-11 3RR5 TITLE DNA LIGASE FROM THE ARCHAEON THERMOCOCCUS SP. 1519 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP]; COMPND 5 EC: 6.5.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS SP. 1519; SOURCE 3 ORGANISM_TAXID: 619742; SOURCE 4 STRAIN: 1519; SOURCE 5 GENE: LIG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DLT1270/PRARE-2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS ATP-DEPENDENT THERMOSTABLE DNA LIGASE, ARCHAEON, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PETROVA,E.Y.BEZSUDNOVA,K.M.BOYKO,A.V.MARDANOV,V.O.POPOV, AUTHOR 2 K.M.POLYAKOV,N.V.RAVIN,I.G.SHABALIN,K.G.SKRYABIN,T.N.STEKHANOVA, AUTHOR 3 M.V.KOVALCHUK REVDAT 4 13-SEP-23 3RR5 1 REMARK SEQADV REVDAT 3 03-APR-13 3RR5 1 JRNL REVDAT 2 05-DEC-12 3RR5 1 JRNL REVDAT 1 11-APR-12 3RR5 0 JRNL AUTH T.PETROVA,E.Y.BEZSUDNOVA,K.M.BOYKO,A.V.MARDANOV, JRNL AUTH 2 K.M.POLYAKOV,V.V.VOLKOV,M.KOZIN,N.V.RAVIN,I.G.SHABALIN, JRNL AUTH 3 K.G.SKRYABIN,T.N.STEKHANOVA,M.V.KOVALCHUK,V.O.POPOV JRNL TITL ATP-DEPENDENT DNA LIGASE FROM THERMOCOCCUS SP. 1519 DISPLAYS JRNL TITL 2 A NEW ARRANGEMENT OF THE OB-FOLD DOMAIN. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 68 1440 2012 JRNL REFN ESSN 1744-3091 JRNL PMID 23192021 JRNL DOI 10.1107/S1744309112043394 REMARK 2 REMARK 2 RESOLUTION. 3.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.2583 - 5.1536 0.99 2824 147 0.2259 0.3023 REMARK 3 2 5.1536 - 4.0942 1.00 2722 129 0.2003 0.2658 REMARK 3 3 4.0942 - 3.5777 1.00 2694 135 0.2381 0.3506 REMARK 3 4 3.5777 - 3.2510 1.00 2663 149 0.2606 0.3184 REMARK 3 5 3.2510 - 3.0183 0.99 2611 155 0.3342 0.3775 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.28 REMARK 3 B_SOL : 45.94 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.900 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.23540 REMARK 3 B22 (A**2) : -5.86880 REMARK 3 B33 (A**2) : 13.10430 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 4191 REMARK 3 ANGLE : 1.319 5679 REMARK 3 CHIRALITY : 0.086 659 REMARK 3 PLANARITY : 0.006 739 REMARK 3 DIHEDRAL : 18.768 1527 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TWO B-FACTORS PER RESIDUES REMARK 4 REMARK 4 3RR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : THE ROTATED-INCLINED DOUBLE REMARK 200 -CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : THE RHODIUM-COATED MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14237 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.257 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.430 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 3GDE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 NA CACODILATE, 0.2 M MGCL2, 20% REMARK 280 GLICEROL, 16% PEG 8000, 100 MM NACL, 50MM TRIS-HCL, PROTEIN 22MG/ REMARK 280 ML (PROTEIN BUFFER: 50MM TRIS-HCL, 100 MM NACL, 0.5 DTT), GEL- REMARK 280 TUBE COUNTER-DIFFUSION METHOD, PH 7.5, LIQUID DIFFUSION, REMARK 280 TEMPERATURE 291K 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 38.47500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.98000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.98000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.47500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.80000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ARG A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 GLY A 11 REMARK 465 LYS A 565 REMARK 465 PHE A 566 REMARK 465 LYS A 567 REMARK 465 ALA A 568 REMARK 465 LYS A 569 REMARK 465 ARG A 570 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 SER A 12 OG REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 50 CG CD OE1 OE2 REMARK 470 TYR A 54 CE1 CE2 CZ OH REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 LYS A 74 CB CG CD CE NZ REMARK 470 ILE A 77 CG1 CG2 CD1 REMARK 470 LYS A 78 CD CE NZ REMARK 470 VAL A 80 CG1 CG2 REMARK 470 SER A 81 OG REMARK 470 MET A 82 SD CE REMARK 470 THR A 84 OG1 CG2 REMARK 470 GLU A 88 CG CD OE1 OE2 REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 GLU A 90 CG CD OE1 OE2 REMARK 470 GLU A 92 CG CD OE1 OE2 REMARK 470 SER A 94 OG REMARK 470 ILE A 95 CG1 CG2 CD1 REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 ASP A 97 OD1 OD2 REMARK 470 THR A 98 OG1 CG2 REMARK 470 GLU A 103 CD OE1 OE2 REMARK 470 VAL A 105 CG1 CG2 REMARK 470 LEU A 109 CG CD1 CD2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 ARG A 112 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 GLN A 114 CG CD OE1 NE2 REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 SER A 116 OG REMARK 470 PHE A 117 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE A 118 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 119 OG REMARK 470 GLN A 120 CG CD OE1 NE2 REMARK 470 ILE A 124 CG1 CG2 CD1 REMARK 470 LYS A 125 CE NZ REMARK 470 SER A 129 OG REMARK 470 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 470 MET A 147 CG SD CE REMARK 470 LYS A 148 CD CE NZ REMARK 470 MET A 155 CB CG SD CE REMARK 470 ASP A 156 CG OD1 OD2 REMARK 470 GLU A 160 CG CD OE1 OE2 REMARK 470 LYS A 163 CE NZ REMARK 470 ILE A 165 CG1 CG2 CD1 REMARK 470 GLU A 195 CG CD OE1 OE2 REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 SER A 223 OG REMARK 470 ILE A 233 CD1 REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 GLU A 246 CG CD OE1 OE2 REMARK 470 LEU A 248 CG CD1 CD2 REMARK 470 ILE A 249 CG2 REMARK 470 TYR A 278 OH REMARK 470 ARG A 287 CD NE CZ NH1 NH2 REMARK 470 SER A 288 OG REMARK 470 ASN A 317 CG OD1 ND2 REMARK 470 ARG A 329 NH1 NH2 REMARK 470 ARG A 331 NE CZ NH1 NH2 REMARK 470 ARG A 332 CZ NH1 NH2 REMARK 470 LYS A 333 CB CG CD CE NZ REMARK 470 ASP A 337 CG OD1 OD2 REMARK 470 MET A 339 CG SD CE REMARK 470 GLU A 341 CG CD OE1 OE2 REMARK 470 GLU A 364 CG CD OE1 OE2 REMARK 470 ARG A 371 NH2 REMARK 470 GLU A 394 CD OE1 OE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 ARG A 415 CG CD NE CZ NH1 NH2 REMARK 470 SER A 418 OG REMARK 470 LYS A 427 CG CD CE NZ REMARK 470 ILE A 444 CD1 REMARK 470 TYR A 465 CE1 CE2 CZ OH REMARK 470 SER A 469 OG REMARK 470 LYS A 492 CE NZ REMARK 470 LYS A 495 CE NZ REMARK 470 ARG A 500 CD NE CZ NH1 NH2 REMARK 470 GLU A 502 CG CD OE1 OE2 REMARK 470 LYS A 504 CG CD CE NZ REMARK 470 PHE A 505 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 511 CG CD CE NZ REMARK 470 ARG A 528 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 542 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 543 CG CD OE1 OE2 REMARK 470 ASP A 544 CG OD1 OD2 REMARK 470 LYS A 545 CG CD CE NZ REMARK 470 SER A 546 OG REMARK 470 GLU A 554 CG CD OE1 OE2 REMARK 470 GLN A 558 CD OE1 NE2 REMARK 470 GLU A 561 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 PRO A 232 C - N - CA ANGL. DEV. = 9.6 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 LYS A 115 -69.93 -124.90 REMARK 500 SER A 116 -75.99 -70.54 REMARK 500 PHE A 117 173.76 179.94 REMARK 500 PHE A 118 -123.82 49.90 REMARK 500 GLN A 120 149.27 69.29 REMARK 500 SER A 142 -75.49 -78.21 REMARK 500 LYS A 148 -70.77 -59.47 REMARK 500 GLU A 160 -71.20 -55.15 REMARK 500 SER A 205 -0.59 81.22 REMARK 500 LEU A 216 -74.23 -83.13 REMARK 500 TYR A 334 -159.11 -140.95 REMARK 500 ILE A 336 -62.34 -127.87 REMARK 500 MET A 436 -129.66 60.28 REMARK 500 VAL A 475 -57.46 -123.04 REMARK 500 PRO A 510 82.25 -67.43 REMARK 500 LYS A 511 -60.53 -107.33 REMARK 500 PHE A 535 57.10 39.68 REMARK 500 VAL A 539 -62.69 -109.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 115 SER A 116 -137.37 REMARK 500 PHE A 117 PHE A 118 147.02 REMARK 500 PHE A 118 SER A 119 -136.10 REMARK 500 ASN A 335 ILE A 336 -129.63 REMARK 500 MET A 436 GLU A 437 -148.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CFM RELATED DB: PDB REMARK 900 ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS REMARK 900 RELATED ID: 3GDE RELATED DB: PDB REMARK 900 THE CLOSED CONFORMATION OF ATP-DEPENDENT DNA LIGASE FROM REMARK 900 ARCHAEOGLOBUS FULGIDUS REMARK 900 RELATED ID: 2HIV RELATED DB: PDB REMARK 900 ATP-DEPENDENT DNA LIGASE FROM S. SOLFATARICUS DBREF 3RR5 A 13 570 UNP C0LJI8 C0LJI8_9EURY 2 559 SEQADV 3RR5 MET A 1 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 ARG A 2 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 GLY A 3 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 SER A 4 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 HIS A 5 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 HIS A 6 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 HIS A 7 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 HIS A 8 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 HIS A 9 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 HIS A 10 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 GLY A 11 UNP C0LJI8 EXPRESSION TAG SEQADV 3RR5 SER A 12 UNP C0LJI8 EXPRESSION TAG SEQRES 1 A 570 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LYS SEQRES 2 A 570 TYR SER GLU LEU ALA ASP LEU TYR ARG ARG LEU GLU LYS SEQRES 3 A 570 THR THR LEU LYS THR LEU LYS THR LYS PHE VAL ALA ASP SEQRES 4 A 570 PHE LEU LYS LYS THR PRO ASP GLU LEU LEU GLU VAL VAL SEQRES 5 A 570 PRO TYR LEU ILE LEU GLY LYS VAL PHE PRO ASP TRP ASP SEQRES 6 A 570 GLU ARG GLU LEU GLY VAL GLY GLU LYS LEU LEU ILE LYS SEQRES 7 A 570 ALA VAL SER MET ALA THR GLY VAL PRO GLU LYS GLU ILE SEQRES 8 A 570 GLU ASN SER ILE LYS ASP THR GLY ASP LEU GLY GLU SER SEQRES 9 A 570 VAL ALA LEU ALA LEU LYS LYS ARG LYS GLN LYS SER PHE SEQRES 10 A 570 PHE SER GLN PRO LEU THR ILE LYS ARG VAL TYR SER THR SEQRES 11 A 570 PHE VAL LYS VAL ALA GLU ALA SER GLY GLU GLY SER GLN SEQRES 12 A 570 ASP ARG LYS MET LYS TYR LEU ALA ASN LEU PHE MET ASP SEQRES 13 A 570 ALA GLN PRO GLU GLU GLY LYS TYR ILE ALA ARG THR VAL SEQRES 14 A 570 LEU GLY THR MET ARG THR GLY VAL ALA GLU GLY ILE LEU SEQRES 15 A 570 ARG ASP ALA ILE ALA GLU ALA PHE ARG VAL LYS PRO GLU SEQRES 16 A 570 LEU VAL GLU ARG ALA TYR MET LEU THR SER ASP PHE GLY SEQRES 17 A 570 TYR VAL ALA LYS VAL ALA LYS LEU GLU GLY ASN GLU GLY SEQRES 18 A 570 LEU SER LYS VAL SER ILE GLN ILE GLY LYS PRO ILE ARG SEQRES 19 A 570 PRO MET LEU ALA GLN ASN ALA ALA SER VAL LYS GLU ALA SEQRES 20 A 570 LEU ILE GLU MET GLY GLY GLU ALA ALA PHE GLU ILE LYS SEQRES 21 A 570 TYR ASP GLY ALA ARG VAL GLN VAL HIS ARG ASP GLY ASP SEQRES 22 A 570 ARG VAL ILE ILE TYR SER ARG ARG LEU GLU ASN VAL THR SEQRES 23 A 570 ARG SER ILE PRO GLU ILE VAL GLU ALA VAL LYS ALA SER SEQRES 24 A 570 LEU LYS PRO SER LYS VAL ILE VAL GLU GLY GLU LEU VAL SEQRES 25 A 570 ALA VAL GLY GLU ASN GLY ARG PRO ARG PRO PHE GLN TYR SEQRES 26 A 570 VAL LEU ARG ARG PHE ARG ARG LYS TYR ASN ILE ASP GLU SEQRES 27 A 570 MET ILE GLU LYS ILE PRO LEU GLU LEU ASN LEU PHE ASP SEQRES 28 A 570 ILE LEU TYR VAL ASP GLY GLU SER LEU ILE ASP THR GLU SEQRES 29 A 570 PHE VAL GLU ARG ARG LYS ARG LEU GLU GLU SER VAL GLU SEQRES 30 A 570 GLU SER GLU LYS ILE LYS ILE ALA GLU GLN LEU VAL THR SEQRES 31 A 570 LYS LYS VAL GLU GLU ALA GLU ALA PHE TYR LYS ARG ALA SEQRES 32 A 570 LEU GLU LEU GLY HIS GLU GLY LEU MET ALA LYS ARG LEU SEQRES 33 A 570 ASP SER VAL TYR GLU PRO GLY ASN ARG GLY LYS LYS TRP SEQRES 34 A 570 LEU LYS ILE LYS PRO THR MET GLU ASN LEU ASP LEU VAL SEQRES 35 A 570 ILE ILE GLY ALA GLU TRP GLY GLU GLY ARG ARG ALA HIS SEQRES 36 A 570 LEU LEU GLY SER PHE LEU VAL ALA ALA TYR ASP PRO ASP SEQRES 37 A 570 SER GLY GLU PHE LEU PRO VAL GLY LYS VAL GLY SER GLY SEQRES 38 A 570 PHE THR ASP GLU ASP LEU VAL GLU PHE THR LYS MET LEU SEQRES 39 A 570 LYS PRO LEU ILE LEU ARG GLU GLU GLY LYS PHE VAL GLU SEQRES 40 A 570 ILE GLU PRO LYS VAL VAL ILE GLU VAL THR TYR GLN GLU SEQRES 41 A 570 ILE GLN LYS SER PRO LYS TYR ARG SER GLY PHE ALA LEU SEQRES 42 A 570 ARG PHE PRO ARG TYR VAL ALA LEU ARG GLU ASP LYS SER SEQRES 43 A 570 PRO GLU GLU ALA ASP THR ILE GLU ARG ILE ALA GLN LEU SEQRES 44 A 570 TYR GLU LEU GLN GLU LYS PHE LYS ALA LYS ARG HET MG A 601 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *4(H2 O) HELIX 1 1 LYS A 13 THR A 27 1 15 HELIX 2 2 LEU A 29 LYS A 43 1 15 HELIX 3 3 GLU A 47 GLU A 50 5 4 HELIX 4 4 VAL A 51 GLY A 58 1 8 HELIX 5 5 GLY A 72 GLY A 85 1 14 HELIX 6 6 PRO A 87 GLY A 99 1 13 HELIX 7 7 ASP A 100 ARG A 112 1 13 HELIX 8 8 THR A 123 ALA A 137 1 15 HELIX 9 9 GLY A 141 MET A 155 1 15 HELIX 10 10 GLN A 158 GLY A 171 1 14 HELIX 11 11 ALA A 178 ARG A 191 1 14 HELIX 12 12 LYS A 193 SER A 205 1 13 HELIX 13 13 ASP A 206 LEU A 216 1 11 HELIX 14 14 GLU A 217 LYS A 224 1 8 HELIX 15 15 SER A 243 MET A 251 1 9 HELIX 16 16 VAL A 285 SER A 288 5 4 HELIX 17 17 ILE A 289 LEU A 300 1 12 HELIX 18 18 PHE A 323 ARG A 332 1 10 HELIX 19 19 ILE A 336 ILE A 343 1 8 HELIX 20 20 GLU A 364 VAL A 376 1 13 HELIX 21 21 LYS A 392 GLY A 407 1 16 HELIX 22 22 GLU A 450 ALA A 454 5 5 HELIX 23 23 THR A 483 LEU A 497 1 15 HELIX 24 24 THR A 552 LEU A 562 1 11 SHEET 1 A 5 LEU A 237 ALA A 241 0 SHEET 2 A 5 ARG A 425 ILE A 432 1 O LYS A 431 N GLN A 239 SHEET 3 A 5 GLY A 410 LYS A 414 -1 N ALA A 413 O LEU A 430 SHEET 4 A 5 ALA A 255 LYS A 260 -1 N GLU A 258 O MET A 412 SHEET 5 A 5 GLN A 387 THR A 390 -1 O LEU A 388 N PHE A 257 SHEET 1 B 5 ARG A 274 TYR A 278 0 SHEET 2 B 5 ALA A 264 ASP A 271 -1 N HIS A 269 O ILE A 276 SHEET 3 B 5 LYS A 304 VAL A 314 -1 O GLY A 309 N VAL A 266 SHEET 4 B 5 LEU A 345 VAL A 355 -1 O GLU A 346 N VAL A 312 SHEET 5 B 5 GLU A 358 SER A 359 -1 O GLU A 358 N VAL A 355 SHEET 1 C 4 PRO A 320 ARG A 321 0 SHEET 2 C 4 LYS A 304 VAL A 314 -1 N ALA A 313 O ARG A 321 SHEET 3 C 4 LEU A 345 VAL A 355 -1 O GLU A 346 N VAL A 312 SHEET 4 C 4 ILE A 382 ILE A 384 1 O LYS A 383 N LEU A 349 SHEET 1 D 5 LEU A 473 VAL A 478 0 SHEET 2 D 5 LEU A 457 ALA A 464 -1 N PHE A 460 O VAL A 478 SHEET 3 D 5 LEU A 439 TRP A 448 -1 N VAL A 442 O ALA A 463 SHEET 4 D 5 PHE A 505 ILE A 508 -1 O ILE A 508 N ILE A 444 SHEET 5 D 5 ILE A 498 GLU A 502 -1 N LEU A 499 O GLU A 507 SHEET 1 E 5 LEU A 473 VAL A 478 0 SHEET 2 E 5 LEU A 457 ALA A 464 -1 N PHE A 460 O VAL A 478 SHEET 3 E 5 LEU A 439 TRP A 448 -1 N VAL A 442 O ALA A 463 SHEET 4 E 5 VAL A 513 THR A 517 -1 O VAL A 516 N LEU A 439 SHEET 5 E 5 ARG A 537 ARG A 542 -1 O ARG A 537 N THR A 517 SHEET 1 F 2 GLU A 520 LYS A 523 0 SHEET 2 F 2 PHE A 531 ARG A 534 -1 O ALA A 532 N GLN A 522 SITE 1 AC1 2 PHE A 323 GLU A 409 CRYST1 76.950 85.600 105.960 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 0.012995 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009438 0.00000