HEADER LIGASE 24-APR-14 4D05 TITLE STRUCTURE AND ACTIVITY OF A MINIMAL-TYPE ATP-DEPENDENT DNA LIGASE FROM TITLE 2 A PSYCHROTOLERANT BACTERIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT DNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: LINK BETWEEN AMP AND LYS173 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSYCHROMONAS SP. SP041; SOURCE 3 ORGANISM_TAXID: 1365007; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHMGWA; SOURCE 10 OTHER_DETAILS: PSYCHROMONAS SP. STRAIN SP041 (GENBANK ACCESSION NO. SOURCE 11 ERP003516) KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.WILLIAMSON,U.ROTHWEILER,H.-K.S.LEIROS REVDAT 4 26-JUN-19 4D05 1 TITLE REMARK DBREF LINK REVDAT 3 28-JUN-17 4D05 1 REMARK ATOM REVDAT 2 19-NOV-14 4D05 1 JRNL REVDAT 1 12-NOV-14 4D05 0 JRNL AUTH A.WILLIAMSON,U.ROTHWEILER,H.-K.S.LEIROS JRNL TITL ENZYME-ADENYLATE STRUCTURE OF A BACTERIAL ATP-DEPENDENT DNA JRNL TITL 2 LIGASE WITH A MINIMIZED DNA-BINDING SURFACE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 3043 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25372693 JRNL DOI 10.1107/S1399004714021099 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 80747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2419 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 24.6124 - 4.2358 1.00 4830 133 0.1592 0.1628 REMARK 3 2 4.2358 - 3.3648 1.00 4679 139 0.1344 0.1866 REMARK 3 3 3.3648 - 2.9403 1.00 4653 148 0.1454 0.2151 REMARK 3 4 2.9403 - 2.6718 1.00 4662 146 0.1415 0.1843 REMARK 3 5 2.6718 - 2.4805 1.00 4588 161 0.1386 0.1878 REMARK 3 6 2.4805 - 2.3344 1.00 4628 139 0.1305 0.1732 REMARK 3 7 2.3344 - 2.2175 1.00 4588 133 0.1294 0.1762 REMARK 3 8 2.2175 - 2.1211 1.00 4608 149 0.1255 0.1793 REMARK 3 9 2.1211 - 2.0395 1.00 4618 126 0.1242 0.1599 REMARK 3 10 2.0395 - 1.9691 1.00 4596 151 0.1363 0.2093 REMARK 3 11 1.9691 - 1.9076 1.00 4568 126 0.1524 0.2144 REMARK 3 12 1.9076 - 1.8531 1.00 4593 162 0.1488 0.1953 REMARK 3 13 1.8531 - 1.8043 0.99 4552 138 0.1566 0.2180 REMARK 3 14 1.8043 - 1.7603 1.00 4544 145 0.1660 0.2127 REMARK 3 15 1.7603 - 1.7203 0.99 4574 139 0.1779 0.2338 REMARK 3 16 1.7203 - 1.6837 0.99 4518 144 0.1936 0.2451 REMARK 3 17 1.6837 - 1.6500 0.98 4529 140 0.2149 0.2830 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.013 4351 REMARK 3 ANGLE : 1.439 5910 REMARK 3 CHIRALITY : 0.101 638 REMARK 3 PLANARITY : 0.007 756 REMARK 3 DIHEDRAL : 15.545 1626 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: NULL REMARK 4 REMARK 4 4D05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-APR-14. REMARK 100 THE DEPOSITION ID IS D_1290060454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80785 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.75 M AMMONIUM SULFATE, 100 MM HEPES REMARK 280 PH 7.4, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 89.21350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.98800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 89.21350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.98800 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 GLY B 0 REMARK 465 GLN B 1 REMARK 465 PRO B 2 REMARK 465 PRO B 3 REMARK 465 PRO B 4 REMARK 465 LYS B 166 REMARK 465 ARG B 167 REMARK 465 ILE B 256 REMARK 465 TYR B 257 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG B 12 CZ NH1 NH2 REMARK 480 VAL B 17 CG1 CG2 REMARK 480 GLN B 19 CB CG CD OE1 NE2 REMARK 480 ILE B 39 CG2 CD1 REMARK 480 GLN B 42 CB CG CD OE1 NE2 REMARK 480 ARG B 80 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 112 CG CD CE NZ REMARK 480 LYS B 132 CE NZ REMARK 480 THR B 165 CB OG1 CG2 REMARK 480 ARG B 169 CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH21 ARG A 30 OD2 ASP A 62 1.38 REMARK 500 OE1 GLU B 207 HD22 ASN B 243 1.54 REMARK 500 O HOH A 2048 O HOH A 2203 1.70 REMARK 500 O HOH A 2048 O HOH A 2082 1.75 REMARK 500 O4 SO4 A 1261 O HOH A 2341 1.77 REMARK 500 O HOH A 2091 O HOH A 2211 1.85 REMARK 500 O HOH A 2273 O HOH A 2283 1.98 REMARK 500 O HOH A 2053 O HOH A 2148 2.01 REMARK 500 O HOH A 2011 O HOH A 2012 2.04 REMARK 500 O HOH A 2437 O HOH A 2452 2.05 REMARK 500 O HOH A 2038 O HOH A 2106 2.05 REMARK 500 NH2 ARG B 109 O ALA B 161 2.10 REMARK 500 O HOH A 2072 O HOH A 2189 2.11 REMARK 500 OD1 ASP B 219 O HOH B 2155 2.12 REMARK 500 O1 SO4 A 1262 O HOH A 2164 2.12 REMARK 500 O HOH B 2152 O HOH B 2166 2.14 REMARK 500 O HOH A 2350 O HOH A 2441 2.15 REMARK 500 NH2 ARG A 30 OD2 ASP A 62 2.17 REMARK 500 O HOH A 2179 O HOH A 2385 2.17 REMARK 500 O HOH A 2169 O HOH A 2368 2.17 REMARK 500 O HOH A 2075 O HOH A 2300 2.17 REMARK 500 OE1 GLU B 129 O HOH B 2097 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2468 O HOH B 2080 3445 2.02 REMARK 500 O HOH A 2410 O HOH B 2067 3445 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MSE B 155 CA - CB - CG ANGL. DEV. = -11.7 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 HIS A 36 -10.53 -146.37 REMARK 500 ASP A 83 108.97 -171.76 REMARK 500 THR A 240 -162.42 -109.59 REMARK 500 VAL A 251 -72.20 -101.82 REMARK 500 HIS B 36 -22.79 -140.89 REMARK 500 SER B 55 -3.42 75.80 REMARK 500 ASP B 83 106.23 -163.61 REMARK 500 GLN B 164 107.60 -164.49 REMARK 500 ARG B 169 -50.64 79.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2111 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A2134 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A2331 DISTANCE = 7.11 ANGSTROMS REMARK 525 HOH B2059 DISTANCE = 6.39 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 AMP B 1260 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1261 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2018 O REMARK 620 2 HOH B2181 O 109.0 REMARK 620 3 PHE B 97 O 104.6 116.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1262 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 1263 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1261 REMARK 999 REMARK 999 SEQUENCE REMARK 999 (GENBANK ACCESSION NO. ERP003516) DBREF 4D05 A 0 257 PDB 4D05 4D05 0 257 DBREF 4D05 B 0 257 PDB 4D05 4D05 0 257 SEQRES 1 A 258 GLY GLN PRO PRO PRO ILE GLN LEU ALA THR ASN TYR ARG SEQRES 2 A 258 GLN ASP ILE ASP VAL THR GLN TYR TYR VAL SER GLU LYS SEQRES 3 A 258 LEU ASP GLY ILE ARG ALA TYR TRP ASN GLY HIS GLN LEU SEQRES 4 A 258 ILE SER LYS GLN GLY ASN ILE PHE THR ALA PRO THR TRP SEQRES 5 A 258 PHE ILE ALA SER PHE PRO THR THR ALA MSE ASP GLY GLU SEQRES 6 A 258 LEU TRP ILE ALA ARG GLN GLN PHE GLU THR VAL SER GLY SEQRES 7 A 258 ILE ALA ARG THR GLN ASP ASN GLN ASN GLU GLN TRP LYS SEQRES 8 A 258 GLN ILE LYS PHE MSE ILE PHE ASP LEU PRO LYS SER THR SEQRES 9 A 258 VAL SER PHE GLU GLN ARG ILE ASN LYS MSE GLN THR LEU SEQRES 10 A 258 VAL THR ASP THR ASN SER PRO TYR LEU GLN MSE ILE GLU SEQRES 11 A 258 GLN GLN LYS ILE PRO ASN THR VAL ALA LEU PHE ASP LEU SEQRES 12 A 258 LEU ASN LYS VAL VAL MSE GLY LYS GLY GLU GLY LEU MSE SEQRES 13 A 258 LEU HIS HIS GLN ASP ALA LEU TYR GLN THR LYS ARG SER SEQRES 14 A 258 ARG ASP LEU MSE LYS LEU LYS LYS PHE GLU ASP ALA GLU SEQRES 15 A 258 ALA THR VAL ILE ALA TYR LEU PRO GLY LYS GLY LYS TYR SEQRES 16 A 258 GLU GLY LEU LEU GLY ALA ILE LEU VAL LYS ASN GLU GLU SEQRES 17 A 258 GLY VAL THR PHE LYS ILE GLY SER GLY PHE SER ASP GLU SEQRES 18 A 258 GLU ARG SER THR PRO PRO PRO ILE GLY SER LEU ILE THR SEQRES 19 A 258 TYR ARG PHE THR GLY LYS THR ASN ASN ASN ILE PRO ARG SEQRES 20 A 258 PHE ALA SER PHE VAL ARG ILE ARG VAL ILE TYR SEQRES 1 B 258 GLY GLN PRO PRO PRO ILE GLN LEU ALA THR ASN TYR ARG SEQRES 2 B 258 GLN ASP ILE ASP VAL THR GLN TYR TYR VAL SER GLU LYS SEQRES 3 B 258 LEU ASP GLY ILE ARG ALA TYR TRP ASN GLY HIS GLN LEU SEQRES 4 B 258 ILE SER LYS GLN GLY ASN ILE PHE THR ALA PRO THR TRP SEQRES 5 B 258 PHE ILE ALA SER PHE PRO THR THR ALA MSE ASP GLY GLU SEQRES 6 B 258 LEU TRP ILE ALA ARG GLN GLN PHE GLU THR VAL SER GLY SEQRES 7 B 258 ILE ALA ARG THR GLN ASP ASN GLN ASN GLU GLN TRP LYS SEQRES 8 B 258 GLN ILE LYS PHE MSE ILE PHE ASP LEU PRO LYS SER THR SEQRES 9 B 258 VAL SER PHE GLU GLN ARG ILE ASN LYS MSE GLN THR LEU SEQRES 10 B 258 VAL THR ASP THR ASN SER PRO TYR LEU GLN MSE ILE GLU SEQRES 11 B 258 GLN GLN LYS ILE PRO ASN THR VAL ALA LEU PHE ASP LEU SEQRES 12 B 258 LEU ASN LYS VAL VAL MSE GLY LYS GLY GLU GLY LEU MSE SEQRES 13 B 258 LEU HIS HIS GLN ASP ALA LEU TYR GLN THR LYS ARG SER SEQRES 14 B 258 ARG ASP LEU MSE LYS LEU LYS LYS PHE GLU ASP ALA GLU SEQRES 15 B 258 ALA THR VAL ILE ALA TYR LEU PRO GLY LYS GLY LYS TYR SEQRES 16 B 258 GLU GLY LEU LEU GLY ALA ILE LEU VAL LYS ASN GLU GLU SEQRES 17 B 258 GLY VAL THR PHE LYS ILE GLY SER GLY PHE SER ASP GLU SEQRES 18 B 258 GLU ARG SER THR PRO PRO PRO ILE GLY SER LEU ILE THR SEQRES 19 B 258 TYR ARG PHE THR GLY LYS THR ASN ASN ASN ILE PRO ARG SEQRES 20 B 258 PHE ALA SER PHE VAL ARG ILE ARG VAL ILE TYR MODRES 4D05 MSE A 61 MET SELENOMETHIONINE MODRES 4D05 MSE A 95 MET SELENOMETHIONINE MODRES 4D05 MSE A 113 MET SELENOMETHIONINE MODRES 4D05 MSE A 127 MET SELENOMETHIONINE MODRES 4D05 MSE A 148 MET SELENOMETHIONINE MODRES 4D05 MSE A 155 MET SELENOMETHIONINE MODRES 4D05 MSE A 172 MET SELENOMETHIONINE MODRES 4D05 MSE B 61 MET SELENOMETHIONINE MODRES 4D05 MSE B 95 MET SELENOMETHIONINE MODRES 4D05 MSE B 113 MET SELENOMETHIONINE MODRES 4D05 MSE B 127 MET SELENOMETHIONINE MODRES 4D05 MSE B 148 MET SELENOMETHIONINE MODRES 4D05 MSE B 155 MET SELENOMETHIONINE MODRES 4D05 MSE B 172 MET SELENOMETHIONINE HET MSE A 61 17 HET MSE A 95 17 HET MSE A 113 17 HET MSE A 127 17 HET MSE A 148 34 HET MSE A 155 17 HET MSE A 172 17 HET MSE B 61 17 HET MSE B 95 17 HET MSE B 113 17 HET MSE B 127 17 HET MSE B 148 34 HET MSE B 155 34 HET MSE B 172 17 HET SO4 A1258 5 HET SO4 A1259 5 HET SO4 A1260 5 HET SO4 A1261 5 HET SO4 A1262 5 HET AMP A1263 34 HET SO4 B1256 5 HET SO4 B1257 5 HET SO4 B1258 5 HET SO4 B1259 5 HET AMP B1260 34 HET MG B1261 1 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 3 SO4 9(O4 S 2-) FORMUL 8 AMP 2(C10 H14 N5 O7 P) FORMUL 14 MG MG 2+ FORMUL 15 HOH *652(H2 O) HELIX 1 1 ASP A 16 THR A 18 5 3 HELIX 2 2 PRO A 49 ALA A 54 1 6 HELIX 3 3 GLN A 71 ARG A 80 1 10 HELIX 4 4 ASN A 86 ILE A 92 5 7 HELIX 5 5 SER A 105 ASN A 121 1 17 HELIX 6 6 ASN A 135 GLY A 149 1 15 HELIX 7 7 LYS A 191 TYR A 194 5 4 HELIX 8 8 SER A 218 THR A 224 1 7 HELIX 9 9 THR A 240 ILE A 244 5 5 HELIX 10 10 ASP B 16 THR B 18 5 3 HELIX 11 11 GLN B 71 THR B 81 1 11 HELIX 12 12 ASN B 86 ILE B 92 5 7 HELIX 13 13 SER B 105 ASN B 121 1 17 HELIX 14 14 ASN B 135 GLY B 149 1 15 HELIX 15 15 LYS B 191 GLU B 195 5 5 HELIX 16 16 SER B 218 THR B 224 1 7 SHEET 1 AA 4 LEU A 7 ASN A 10 0 SHEET 2 AA 4 ARG A 167 LEU A 174 1 N SER A 168 O LEU A 7 SHEET 3 AA 4 GLY A 153 HIS A 158 -1 O LEU A 154 N LEU A 174 SHEET 4 AA 4 TYR A 20 LYS A 25 -1 O TYR A 21 N HIS A 157 SHEET 1 AB 5 LEU A 38 ILE A 39 0 SHEET 2 AB 5 ILE A 29 TRP A 33 -1 O TYR A 32 N ILE A 39 SHEET 3 AB 5 MSE A 61 TRP A 66 -1 O MSE A 61 N TRP A 33 SHEET 4 AB 5 LYS A 93 ASP A 98 -1 O LYS A 93 N TRP A 66 SHEET 5 AB 5 LEU A 125 MSE A 127 1 O GLN A 126 N ILE A 96 SHEET 1 AC 5 THR A 210 ILE A 213 0 SHEET 2 AC 5 LEU A 198 ASN A 205 -1 O ILE A 201 N ILE A 213 SHEET 3 AC 5 GLU A 178 PRO A 189 -1 O THR A 183 N LYS A 204 SHEET 4 AC 5 LEU A 231 PHE A 236 -1 O ILE A 232 N ALA A 182 SHEET 5 AC 5 SER A 249 VAL A 255 -1 O SER A 249 N ARG A 235 SHEET 1 BA 5 THR B 9 ASN B 10 0 SHEET 2 BA 5 LEU B 171 LYS B 175 1 O LEU B 171 N THR B 9 SHEET 3 BA 5 GLY B 153 HIS B 158 -1 O LEU B 154 N LEU B 174 SHEET 4 BA 5 TYR B 20 GLU B 24 -1 O TYR B 21 N HIS B 157 SHEET 5 BA 5 GLN B 131 LYS B 132 -1 O GLN B 131 N VAL B 22 SHEET 1 BB 5 LEU B 38 ILE B 39 0 SHEET 2 BB 5 ILE B 29 TRP B 33 -1 O TYR B 32 N ILE B 39 SHEET 3 BB 5 MSE B 61 TRP B 66 -1 O MSE B 61 N TRP B 33 SHEET 4 BB 5 LYS B 93 ASP B 98 -1 O LYS B 93 N TRP B 66 SHEET 5 BB 5 LEU B 125 MSE B 127 1 O GLN B 126 N ILE B 96 SHEET 1 BC 5 THR B 210 ILE B 213 0 SHEET 2 BC 5 LEU B 198 ASN B 205 -1 O ILE B 201 N ILE B 213 SHEET 3 BC 5 GLU B 178 PRO B 189 -1 O THR B 183 N LYS B 204 SHEET 4 BC 5 LEU B 231 PHE B 236 -1 O ILE B 232 N ALA B 182 SHEET 5 BC 5 SER B 249 ILE B 253 -1 O SER B 249 N ARG B 235 LINK C ALA A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N AASP A 62 1555 1555 1.34 LINK C MSE A 61 N BASP A 62 1555 1555 1.33 LINK C PHE A 94 N MSE A 95 1555 1555 1.33 LINK C MSE A 95 N ILE A 96 1555 1555 1.33 LINK C LYS A 112 N MSE A 113 1555 1555 1.33 LINK C MSE A 113 N GLN A 114 1555 1555 1.34 LINK C GLN A 126 N MSE A 127 1555 1555 1.34 LINK C MSE A 127 N ILE A 128 1555 1555 1.32 LINK C VAL A 147 N AMSE A 148 1555 1555 1.32 LINK C VAL A 147 N BMSE A 148 1555 1555 1.33 LINK C AMSE A 148 N GLY A 149 1555 1555 1.32 LINK C BMSE A 148 N GLY A 149 1555 1555 1.33 LINK C LEU A 154 N MSE A 155 1555 1555 1.33 LINK C MSE A 155 N LEU A 156 1555 1555 1.34 LINK C LEU A 171 N MSE A 172 1555 1555 1.32 LINK C MSE A 172 N LYS A 173 1555 1555 1.33 LINK C ALA B 60 N MSE B 61 1555 1555 1.34 LINK C MSE B 61 N ASP B 62 1555 1555 1.34 LINK C PHE B 94 N MSE B 95 1555 1555 1.33 LINK C MSE B 95 N ILE B 96 1555 1555 1.33 LINK C LYS B 112 N MSE B 113 1555 1555 1.33 LINK C MSE B 113 N GLN B 114 1555 1555 1.33 LINK C GLN B 126 N MSE B 127 1555 1555 1.32 LINK C MSE B 127 N ILE B 128 1555 1555 1.32 LINK C VAL B 147 N BMSE B 148 1555 1555 1.33 LINK C VAL B 147 N AMSE B 148 1555 1555 1.34 LINK C BMSE B 148 N GLY B 149 1555 1555 1.33 LINK C AMSE B 148 N GLY B 149 1555 1555 1.33 LINK C LEU B 154 N BMSE B 155 1555 1555 1.32 LINK C LEU B 154 N AMSE B 155 1555 1555 1.32 LINK C BMSE B 155 N LEU B 156 1555 1555 1.33 LINK C AMSE B 155 N LEU B 156 1555 1555 1.34 LINK C LEU B 171 N MSE B 172 1555 1555 1.33 LINK C MSE B 172 N LYS B 173 1555 1555 1.33 LINK MG MG B1261 O HOH B2018 1555 1555 2.80 LINK MG MG B1261 O HOH B2181 1555 1555 2.84 LINK MG MG B1261 O PHE B 97 1555 1555 2.89 LINK NZ LYS A 25 P AMP A1263 1555 1555 1.95 SITE 1 AC1 7 GLN A 70 GLN A 71 PHE A 72 GLU A 73 SITE 2 AC1 7 HOH A2090 HOH A2195 HOH A2382 SITE 1 AC2 6 GLY A 214 SER A 215 ARG A 252 ARG A 254 SITE 2 AC2 6 HOH A2411 HOH A2458 SITE 1 AC3 6 GLN B 70 GLN B 71 PHE B 72 GLU B 73 SITE 2 AC3 6 HOH B2027 HOH B2069 SITE 1 AC4 5 LYS B 145 SER B 215 GLY B 216 PHE B 217 SITE 2 AC4 5 ARG B 222 SITE 1 AC5 7 LYS A 204 HOH A2405 HOH A2408 HOH A2467 SITE 2 AC5 7 PHE B 211 LYS B 212 HOH B2148 SITE 1 AC6 4 SER B 102 THR B 103 VAL B 104 HOH B2180 SITE 1 AC7 7 LYS A 41 ARG A 167 LYS A 173 AMP A1263 SITE 2 AC7 7 HOH A2025 HOH A2101 HOH A2341 SITE 1 AC8 5 GLN B 71 ARG B 252 ARG B 254 VAL B 255 SITE 2 AC8 5 HOH B2064 SITE 1 AC9 6 THR A 59 ALA A 60 HOH A2164 HOH A2166 SITE 2 AC9 6 HOH A2247 HOH A2267 SITE 1 BC1 19 SER A 23 GLU A 24 LYS A 25 LEU A 26 SITE 2 BC1 19 ARG A 30 GLU A 64 PHE A 97 GLU A 152 SITE 3 BC1 19 MSE A 155 LYS A 173 SO4 A1261 HOH A2025 SITE 4 BC1 19 HOH A2071 HOH A2078 HOH A2100 HOH A2101 SITE 5 BC1 19 HOH A2127 HOH A2469 HOH A2470 SITE 1 BC2 11 SER B 23 GLU B 24 LYS B 25 LEU B 26 SITE 2 BC2 11 ARG B 30 GLU B 64 PHE B 97 ILE B 128 SITE 3 BC2 11 MSE B 155 LYS B 173 HOH B2018 SITE 1 BC3 5 PHE B 97 PHE B 106 HIS B 157 HOH B2018 SITE 2 BC3 5 HOH B2181 CRYST1 178.427 43.976 89.633 90.00 105.92 90.00 C 1 2 1 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 0.005605 0.000000 0.001599 0.00000 SCALE2 0.000000 0.022740 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011602 0.00000