HEADER LIGASE 18-APR-12 4EQ5 TITLE DNA LIGASE FROM THE ARCHAEON THERMOCOCCUS SIBIRICUS 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 SIBIRICUS; SOURCE 3 ORGANISM_TAXID: 604354; SOURCE 4 STRAIN: MM 739; SOURCE 5 GENE: LIG, THERMOSTABLE ATP-DEPENDENT DNA LIGASE GENE TSIB_0885, SOURCE 6 TSIB_0885; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: DLT1270/PRARE-2; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS DNA-BINDING DOMAIN, ADENYLATION DOMAIN, ATP-DEPENDENT THERMOSTABLE KEYWDS 2 DNA LIGASE, ARCHAEON THERMOCOCCUS SIBIRICUS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PETROVA,E.Y.BEZSUDNOVA,B.D.DOROKHOV,E.S.SLUTSKAYA,K.M.POLYAKOV, AUTHOR 2 P.V.DOROVATOVSKIY,N.V.RAVIN,K.G.SKRYABIN,M.V.KOVALCHUK,V.O.POPOV REVDAT 2 13-SEP-23 4EQ5 1 REMARK SEQADV REVDAT 1 09-MAY-12 4EQ5 0 JRNL AUTH T.E.PETROVA,E.Y.BEZSUDNOVA,B.D.DOROKHOV,E.S.SLUTSKAYA, JRNL AUTH 2 K.M.POLYAKOV,P.V.DOROVATOVSKIY,N.V.RAVIN,K.G.SKRYABIN, JRNL AUTH 3 M.V.KOVALCHUK,V.O.POPOV JRNL TITL EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY JRNL TITL 2 CRYSTALLOGRAPHIC ANALYSIS OF A THERMOSTABLE DNA LIGASE FROM JRNL TITL 3 THE ARCHAEON THERMOCOCCUS SIBIRICUS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 68 163 2012 JRNL REFN ESSN 1744-3091 JRNL PMID 22297989 JRNL DOI 10.1107/S1744309111050913 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 15576 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.273 REMARK 3 FREE R VALUE : 0.358 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 797 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 29.2965 - 5.1710 0.99 2623 112 0.2413 0.2900 REMARK 3 2 5.1710 - 4.1080 0.98 2454 130 0.2437 0.3853 REMARK 3 3 4.1080 - 3.5898 0.98 2414 148 0.2784 0.3531 REMARK 3 4 3.5898 - 3.2620 0.99 2445 134 0.3040 0.3875 REMARK 3 5 3.2620 - 3.0285 1.00 2419 144 0.3437 0.3762 REMARK 3 6 3.0285 - 2.8501 1.00 2424 129 0.3957 0.4524 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 : 65.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.040 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 31.47770 REMARK 3 B22 (A**2) : -18.72360 REMARK 3 B33 (A**2) : -12.75410 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 : 0.010 3949 REMARK 3 ANGLE : 1.500 5347 REMARK 3 CHIRALITY : 0.093 614 REMARK 3 PLANARITY : 0.007 687 REMARK 3 DIHEDRAL : 21.718 1439 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: RELATIVELY LOW NUMBER OF OBSERVATIONS REMARK 3 DID NOT ALLOW TO PERFORM REFINEMENT OF B-FACTORS FOR EACH ATOM. REMARK 3 ONE B-FACTOR WAS REFINED FOR EACH RESIDUE REMARK 4 REMARK 4 4EQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-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 : KURCHATOV SNC REMARK 200 BEAMLINE : K4.4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.985 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX SX-165MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DNA REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18232 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.050 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 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 : 0.970 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 2CFM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085 M HEPES, 8.5% 2-PROPANOL (V/V), REMARK 280 17% (W/V) PEG 4000, 15% (V/V) GLYCEROL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 29.29500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.77000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.29500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.77000 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 GLY A 73 REMARK 465 GLU A 74 REMARK 465 LYS A 75 REMARK 465 MET A 83 REMARK 465 ALA A 84 REMARK 465 THR A 85 REMARK 465 GLY A 86 REMARK 465 ILE A 87 REMARK 465 ASN A 88 REMARK 465 SER A 89 REMARK 465 GLU A 90 REMARK 465 GLU A 91 REMARK 465 ILE A 92 REMARK 465 GLU A 93 REMARK 465 ASN A 94 REMARK 465 SER A 95 REMARK 465 VAL A 96 REMARK 465 ARG A 97 REMARK 465 ASP A 98 REMARK 465 THR A 99 REMARK 465 GLY A 100 REMARK 465 ASP A 101 REMARK 465 LEU A 102 REMARK 465 GLY A 103 REMARK 465 GLU A 104 REMARK 465 SER A 105 REMARK 465 ILE A 106 REMARK 465 ALA A 107 REMARK 465 LEU A 108 REMARK 465 ALA A 109 REMARK 465 LEU A 110 REMARK 465 ASN A 111 REMARK 465 LYS A 112 REMARK 465 ARG A 113 REMARK 465 LYS A 114 REMARK 465 GLN A 115 REMARK 465 LYS A 116 REMARK 465 SER A 117 REMARK 465 PHE A 118 REMARK 465 PHE A 119 REMARK 465 SER A 120 REMARK 465 GLN A 121 REMARK 465 PRO A 122 REMARK 465 LEU A 123 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 LEU A 13 CB CG CD1 CD2 REMARK 470 LYS A 15 CD CE NZ REMARK 470 VAL A 18 CG1 CG2 REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 ARG A 23 NE CZ NH1 NH2 REMARK 470 SER A 43 OG REMARK 470 GLU A 45 CG CD OE1 OE2 REMARK 470 LYS A 46 CD CE NZ REMARK 470 PRO A 47 CG CD REMARK 470 GLU A 48 CG CD OE1 OE2 REMARK 470 LEU A 49 CG CD1 CD2 REMARK 470 LEU A 50 CG CD1 CD2 REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 VAL A 52 CG1 CG2 REMARK 470 LEU A 70 CG CD1 CD2 REMARK 470 ILE A 72 CD1 REMARK 470 LEU A 76 CG CD1 CD2 REMARK 470 LEU A 77 CG CD1 CD2 REMARK 470 ILE A 78 CG1 CG2 CD1 REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 VAL A 81 CG1 CG2 REMARK 470 SER A 82 OG REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 ARG A 127 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 130 CG OD1 ND2 REMARK 470 LEU A 132 CG CD1 CD2 REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 ILE A 135 CD1 REMARK 470 GLU A 137 CG CD OE1 OE2 REMARK 470 SER A 139 OG REMARK 470 SER A 143 OG REMARK 470 GLN A 144 CG CD OE1 NE2 REMARK 470 ASP A 145 CG OD1 OD2 REMARK 470 ARG A 146 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 LEU A 148 CG CD1 CD2 REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 TYR A 150 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 151 CG CD1 CD2 REMARK 470 ASN A 153 CG OD1 ND2 REMARK 470 LEU A 154 CG CD1 CD2 REMARK 470 PHE A 155 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 157 CG OD1 OD2 REMARK 470 SER A 159 OG REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 TYR A 165 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 170 CG1 CG2 REMARK 470 ILE A 173 CG1 CG2 CD1 REMARK 470 MET A 174 CG SD CE REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 THR A 176 OG1 CG2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 LYS A 227 CE NZ REMARK 470 ASN A 244 CG OD1 ND2 REMARK 470 GLU A 247 CD OE1 OE2 REMARK 470 ASN A 272 ND2 REMARK 470 LYS A 288 CG CD CE NZ REMARK 470 ARG A 296 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 ARG A 332 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 334 CG CD CE NZ REMARK 470 GLU A 338 CG CD OE1 OE2 REMARK 470 GLU A 339 CG CD OE1 OE2 REMARK 470 ILE A 341 CG1 CG2 CD1 REMARK 470 GLU A 342 CD OE1 OE2 REMARK 470 ILE A 353 CD1 REMARK 470 ASN A 360 OD1 ND2 REMARK 470 GLU A 368 CD OE1 OE2 REMARK 470 ASN A 378 OD1 ND2 REMARK 470 SER A 379 OG REMARK 470 LYS A 384 CG CD CE NZ REMARK 470 SER A 393 OG REMARK 470 GLU A 410 CD OE1 OE2 REMARK 470 GLU A 448 CG CD OE1 OE2 REMARK 470 SER A 455 OG REMARK 470 SER A 459 CB OG REMARK 470 SER A 460 OG REMARK 470 ASP A 472 CG OD1 OD2 REMARK 470 SER A 481 OG REMARK 470 LYS A 500 CE NZ REMARK 470 GLU A 508 CD OE1 OE2 REMARK 470 LYS A 527 CG CD CE NZ REMARK 470 TYR A 539 OH REMARK 470 PHE A 563 CE1 CE2 CZ REMARK 470 ARG A 571 CD NE CZ NH1 NH2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 PRO A 47 REMARK 475 ALA A 138 REMARK 475 ASP A 157 REMARK 475 ALA A 158 REMARK 475 SER A 159 REMARK 475 MET A 174 REMARK 475 ARG A 175 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 47 C - N - CA ANGL. DEV. = 12.2 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 LYS A 30 -70.07 -51.55 REMARK 500 LYS A 46 56.47 -113.56 REMARK 500 LEU A 49 -21.86 -38.73 REMARK 500 LEU A 50 3.14 85.56 REMARK 500 GLU A 51 -78.04 -53.14 REMARK 500 VAL A 52 -121.00 33.24 REMARK 500 GLU A 67 -5.32 71.11 REMARK 500 GLU A 137 -77.24 -49.53 REMARK 500 ALA A 138 63.37 27.05 REMARK 500 GLN A 144 -77.75 -120.51 REMARK 500 ASP A 145 -72.74 -61.70 REMARK 500 ARG A 146 -134.99 41.31 REMARK 500 LYS A 147 -10.12 61.22 REMARK 500 LEU A 217 -63.95 -100.37 REMARK 500 ASP A 220 -79.63 -50.78 REMARK 500 GLU A 221 -114.60 36.19 REMARK 500 HIS A 409 -84.12 -112.73 REMARK 500 GLU A 410 -58.30 -137.35 REMARK 500 LYS A 470 -53.71 -151.93 REMARK 500 ASP A 472 11.42 -35.71 REMARK 500 PHE A 473 84.96 73.50 REMARK 500 PRO A 526 48.18 -79.07 REMARK 500 PHE A 536 77.60 53.19 REMARK 500 LYS A 568 -64.87 -92.98 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 GLU A 45 LYS A 46 -146.17 REMARK 500 LYS A 46 PRO A 47 144.22 REMARK 500 GLU A 48 LEU A 49 -126.76 REMARK 500 GLU A 51 VAL A 52 128.46 REMARK 500 GLU A 137 ALA A 138 142.78 REMARK 500 GLY A 140 ALA A 141 -139.83 REMARK 500 ASP A 220 GLU A 221 132.41 REMARK 500 VAL A 469 LYS A 470 139.16 REMARK 500 LYS A 470 GLY A 471 -140.41 REMARK 500 GLY A 471 ASP A 472 -140.33 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 AMP 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 REMARK 900 RELATED ID: 3RR5 RELATED DB: PDB REMARK 900 DNA LIGASE FROM THE ARCHAEON THERMOCOCCUS SP. 1519 DBREF 4EQ5 A 13 571 UNP C6A2U9 C6A2U9_THESM 2 560 SEQADV 4EQ5 MET A 1 UNP C6A2U9 INITIATING METHIONINE SEQADV 4EQ5 ARG A 2 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 GLY A 3 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 SER A 4 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 HIS A 5 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 HIS A 6 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 HIS A 7 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 HIS A 8 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 HIS A 9 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 HIS A 10 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 GLY A 11 UNP C6A2U9 EXPRESSION TAG SEQADV 4EQ5 SER A 12 UNP C6A2U9 EXPRESSION TAG SEQRES 1 A 571 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LEU SEQRES 2 A 571 TYR LYS GLU LEU VAL GLU LEU TYR LYS ARG LEU GLU LYS SEQRES 3 A 571 THR THR LEU LYS THR LEU LYS THR LYS PHE VAL SER ASP SEQRES 4 A 571 PHE LEU LYS SER VAL GLU LYS PRO GLU LEU LEU GLU VAL SEQRES 5 A 571 ILE PRO TYR LEU ILE LEU GLY LYS VAL PHE PRO ASP TRP SEQRES 6 A 571 ASP GLU ARG GLU LEU GLY ILE GLY GLU LYS LEU LEU ILE SEQRES 7 A 571 LYS ALA VAL SER MET ALA THR GLY ILE ASN SER GLU GLU SEQRES 8 A 571 ILE GLU ASN SER VAL ARG ASP THR GLY ASP LEU GLY GLU SEQRES 9 A 571 SER ILE ALA LEU ALA LEU ASN LYS ARG LYS GLN LYS SER SEQRES 10 A 571 PHE PHE SER GLN PRO LEU THR ILE GLU ARG VAL TYR ASN SEQRES 11 A 571 THR LEU VAL LYS ILE ALA GLU ALA SER GLY ALA GLY SER SEQRES 12 A 571 GLN ASP ARG LYS LEU LYS TYR LEU ALA ASN LEU PHE MET SEQRES 13 A 571 ASP ALA SER PRO ASP GLU GLY LYS TYR LEU ALA ARG THR SEQRES 14 A 571 VAL LEU GLY ILE MET ARG THR GLY VAL ALA GLU GLY LEU SEQRES 15 A 571 LEU ARG ASP ALA LEU ALA ASP ALA PHE LYS VAL ARG VAL SEQRES 16 A 571 GLU LEU VAL GLU ARG ALA TYR MET LEU THR SER ASP PHE SEQRES 17 A 571 GLY PHE VAL ALA LYS VAL ALA LYS LEU GLU GLY ASP GLU SEQRES 18 A 571 GLY LEU ALA LYS VAL LYS ILE GLN VAL GLY LYS PRO ILE SEQRES 19 A 571 LYS PRO MET LEU ALA GLN MET ALA ALA ASN VAL ARG GLU SEQRES 20 A 571 ALA LEU VAL GLU MET GLY GLY GLU ALA GLU PHE GLU ILE SEQRES 21 A 571 LYS TYR ASP GLY ALA ARG VAL GLN VAL HIS LYS ASN GLY SEQRES 22 A 571 ASN LYS VAL LEU ILE TYR SER ARG ARG LEU GLU ASN VAL SEQRES 23 A 571 THR LYS SER ILE PRO GLU VAL VAL GLU ARG VAL LYS GLU SEQRES 24 A 571 ALA LEU LYS PRO GLU LYS VAL ILE VAL GLU GLY GLU LEU SEQRES 25 A 571 VAL ALA VAL GLU GLU THR GLY ARG PRO ARG PRO PHE GLN SEQRES 26 A 571 TYR VAL LEU ARG ARG PHE ARG ARG LYS TYR ASN ILE GLU SEQRES 27 A 571 GLU MET ILE GLU LYS ILE PRO LEU GLU LEU ASN LEU PHE SEQRES 28 A 571 ASP ILE LEU TYR VAL ASP GLY GLN ASN MET ILE ASP THR SEQRES 29 A 571 PRO PHE MET GLU ARG ARG LYS VAL LEU GLU SER VAL VAL SEQRES 30 A 571 ASN SER ASN GLU TRP ILE LYS SER ALA GLU ASN LEU ILE SEQRES 31 A 571 THR LYS SER PRO GLU GLU ALA GLU ALA PHE TYR HIS LYS SEQRES 32 A 571 ALA LEU ASP LEU GLY HIS GLU GLY LEU MET ALA LYS ARG SEQRES 33 A 571 LEU ASP SER THR TYR GLU PRO GLY ASN ARG GLY LYS LYS SEQRES 34 A 571 TRP LEU LYS ILE LYS PRO THR MET GLU ASN LEU ASP LEU SEQRES 35 A 571 VAL VAL LEU GLY ALA GLU TRP GLY GLU GLY ARG ARG SER SEQRES 36 A 571 GLY VAL LEU SER SER PHE LEU LEU GLY ALA TYR ASP PRO SEQRES 37 A 571 VAL LYS GLY ASP PHE VAL PRO VAL GLY LYS VAL GLY SER SEQRES 38 A 571 GLY PHE THR ASP GLU ASP LEU VAL GLU PHE THR LYS MET SEQRES 39 A 571 LEU LYS PRO LEU ILE LYS LYS GLU HIS GLY LYS GLU VAL SEQRES 40 A 571 GLU LEU GLU PRO LYS VAL VAL ILE GLU VAL ALA TYR GLN SEQRES 41 A 571 GLU ILE GLN LYS SER PRO LYS TYR GLU SER GLY PHE ALA SEQRES 42 A 571 LEU ARG PHE PRO ARG TYR ILE ALA LEU ARG GLU ASP LYS SEQRES 43 A 571 GLY PRO GLU ASP ALA ASP THR VAL GLN ARG LEU ALA GLU SEQRES 44 A 571 LEU TYR GLN PHE GLN GLU ARG LEU LYS GLY GLY ARG HET AMP A 601 23 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 HOH *2(H2 O) HELIX 1 1 LEU A 13 LYS A 26 1 14 HELIX 2 2 LEU A 29 SER A 43 1 15 HELIX 3 3 VAL A 52 GLY A 59 1 8 HELIX 4 4 ILE A 125 GLU A 137 1 13 HELIX 5 5 LYS A 147 MET A 156 1 10 HELIX 6 6 SER A 159 LEU A 171 1 13 HELIX 7 7 ALA A 179 PHE A 191 1 13 HELIX 8 8 ARG A 194 SER A 206 1 13 HELIX 9 9 ASP A 207 GLY A 219 1 13 HELIX 10 10 GLY A 219 VAL A 226 1 8 HELIX 11 11 ASN A 244 MET A 252 1 9 HELIX 12 12 VAL A 286 SER A 289 5 4 HELIX 13 13 ILE A 290 LEU A 301 1 12 HELIX 14 14 PRO A 323 ARG A 333 1 11 HELIX 15 15 ASN A 336 ILE A 344 1 9 HELIX 16 16 PRO A 365 VAL A 377 1 13 HELIX 17 17 SER A 393 LEU A 407 1 15 HELIX 18 18 GLU A 451 GLY A 456 5 6 HELIX 19 19 THR A 484 LYS A 496 1 13 HELIX 20 20 GLY A 547 ALA A 551 5 5 HELIX 21 21 THR A 553 GLY A 570 1 18 SHEET 1 A 5 LEU A 238 MET A 241 0 SHEET 2 A 5 ARG A 426 ILE A 433 1 O LYS A 432 N GLN A 240 SHEET 3 A 5 GLY A 411 LYS A 415 -1 N LEU A 412 O ILE A 433 SHEET 4 A 5 ALA A 256 LYS A 261 -1 N GLU A 257 O LYS A 415 SHEET 5 A 5 ASN A 388 THR A 391 -1 O LEU A 389 N PHE A 258 SHEET 1 B 5 LYS A 275 TYR A 279 0 SHEET 2 B 5 ALA A 265 ASN A 272 -1 N HIS A 270 O LEU A 277 SHEET 3 B 5 LYS A 305 ALA A 314 -1 O VAL A 308 N VAL A 269 SHEET 4 B 5 LEU A 346 VAL A 356 -1 O GLU A 347 N VAL A 313 SHEET 5 B 5 GLN A 359 ASN A 360 -1 O GLN A 359 N VAL A 356 SHEET 1 C 5 LYS A 275 TYR A 279 0 SHEET 2 C 5 ALA A 265 ASN A 272 -1 N HIS A 270 O LEU A 277 SHEET 3 C 5 LYS A 305 ALA A 314 -1 O VAL A 308 N VAL A 269 SHEET 4 C 5 LEU A 346 VAL A 356 -1 O GLU A 347 N VAL A 313 SHEET 5 C 5 ILE A 383 SER A 385 1 O LYS A 384 N LEU A 350 SHEET 1 D 5 PRO A 475 VAL A 479 0 SHEET 2 D 5 LEU A 458 GLY A 464 -1 N LEU A 463 O VAL A 476 SHEET 3 D 5 LEU A 440 TRP A 449 -1 N GLU A 448 O SER A 460 SHEET 4 D 5 GLU A 506 LEU A 509 -1 O VAL A 507 N ALA A 447 SHEET 5 D 5 ILE A 499 HIS A 503 -1 N LYS A 500 O GLU A 508 SHEET 1 E 5 PRO A 475 VAL A 479 0 SHEET 2 E 5 LEU A 458 GLY A 464 -1 N LEU A 463 O VAL A 476 SHEET 3 E 5 LEU A 440 TRP A 449 -1 N GLU A 448 O SER A 460 SHEET 4 E 5 VAL A 514 GLN A 523 -1 O ILE A 515 N LEU A 442 SHEET 5 E 5 ALA A 533 LEU A 542 -1 O ARG A 535 N GLU A 521 SITE 1 AC1 12 LEU A 238 GLU A 259 ILE A 260 LYS A 261 SITE 2 AC1 12 TYR A 262 ARG A 266 ARG A 281 GLU A 311 SITE 3 AC1 12 PHE A 351 LYS A 415 ARG A 426 LYS A 432 CRYST1 58.590 87.540 126.300 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 0.017068 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007918 0.00000