HEADER HYDROLASE 04-AUG-11 3TAZ TITLE CRYSTAL STRUCTURE OF NURA BOUND TO DAMP AND MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DOUBLE-STRAND BREAK REPAIR PROTEIN NURA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 5 GENE: PF1168; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS RECOMBINATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.CHAE,Y.C.KIM,Y.CHO REVDAT 4 05-JUN-24 3TAZ 1 REMARK HET ATOM REVDAT 3 20-MAR-24 3TAZ 1 REMARK SEQADV LINK REVDAT 2 03-JUL-13 3TAZ 1 JRNL REVDAT 1 23-NOV-11 3TAZ 0 JRNL AUTH J.CHAE,Y.C.KIM,Y.CHO JRNL TITL CRYSTAL STRUCTURE OF THE NURA-DAMP-MN2+ COMPLEX JRNL REF NUCLEIC ACIDS RES. V. 40 2258 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22064858 JRNL DOI 10.1093/NAR/GKR999 REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 15536 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 784 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 28.7129 - 5.8019 1.00 2619 137 0.1900 0.2551 REMARK 3 2 5.8019 - 4.6113 1.00 2531 130 0.1885 0.2815 REMARK 3 3 4.6113 - 4.0302 0.99 2466 136 0.1725 0.2881 REMARK 3 4 4.0302 - 3.6625 0.99 2433 133 0.2006 0.2696 REMARK 3 5 3.6625 - 3.4005 0.97 2381 131 0.2012 0.3292 REMARK 3 6 3.4005 - 3.2003 0.94 2322 117 0.2290 0.3338 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 84.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 98.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 109.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.67600 REMARK 3 B22 (A**2) : 16.56210 REMARK 3 B33 (A**2) : -11.88610 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 7132 REMARK 3 ANGLE : 1.456 9623 REMARK 3 CHIRALITY : 0.092 1109 REMARK 3 PLANARITY : 0.006 1205 REMARK 3 DIHEDRAL : 19.886 2749 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 56.7886 65.3059 92.6556 REMARK 3 T TENSOR REMARK 3 T11: 0.2532 T22: 0.2191 REMARK 3 T33: 0.2846 T12: 0.0418 REMARK 3 T13: -0.0389 T23: -0.0457 REMARK 3 L TENSOR REMARK 3 L11: 0.8360 L22: 0.3827 REMARK 3 L33: 2.0896 L12: 0.3242 REMARK 3 L13: -0.0741 L23: 0.1843 REMARK 3 S TENSOR REMARK 3 S11: 0.0147 S12: -0.0917 S13: 0.1202 REMARK 3 S21: 0.0016 S22: -0.1022 S23: 0.0223 REMARK 3 S31: 0.0006 S32: 0.1384 S33: 0.0416 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 3TAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15913 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.7_650 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 400, 0.1M TRIS-HCL, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K 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 32.57900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.70700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.42350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.70700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.57900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.42350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 ALA A 224 REMARK 465 LEU A 225 REMARK 465 GLY A 226 REMARK 465 TYR A 227 REMARK 465 GLY A 309 REMARK 465 VAL A 310 REMARK 465 GLU A 311 REMARK 465 PHE A 442 REMARK 465 VAL A 443 REMARK 465 LYS A 444 REMARK 465 TYR A 445 REMARK 465 GLY A 446 REMARK 465 ARG A 447 REMARK 465 SER A 448 REMARK 465 PRO A 449 REMARK 465 LEU A 450 REMARK 465 GLU A 451 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 TYR B 211 REMARK 465 GLY B 212 REMARK 465 SER B 213 REMARK 465 GLY B 214 REMARK 465 LEU B 308 REMARK 465 GLY B 309 REMARK 465 PHE B 442 REMARK 465 VAL B 443 REMARK 465 LYS B 444 REMARK 465 TYR B 445 REMARK 465 GLY B 446 REMARK 465 ARG B 447 REMARK 465 SER B 448 REMARK 465 PRO B 449 REMARK 465 LEU B 450 REMARK 465 GLU B 451 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 LYS B 215 CG CD CE NZ 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 O ARG A 241 OD2 ASP B 246 2.13 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 6 -17.51 65.58 REMARK 500 ASN A 26 70.23 54.82 REMARK 500 GLU A 27 -73.46 -81.81 REMARK 500 SER A 60 -130.83 43.71 REMARK 500 VAL A 138 80.23 57.62 REMARK 500 TYR A 139 148.47 -170.75 REMARK 500 LEU A 162 -71.08 -48.26 REMARK 500 GLU A 181 -71.29 -48.76 REMARK 500 ILE A 204 -65.05 -105.22 REMARK 500 VAL A 231 78.01 43.72 REMARK 500 TYR A 300 176.70 171.13 REMARK 500 THR A 301 160.93 177.73 REMARK 500 ALA A 305 -62.31 -98.80 REMARK 500 LEU A 325 -76.37 -123.32 REMARK 500 HIS A 328 -74.25 -55.04 REMARK 500 GLN A 375 -131.67 48.53 REMARK 500 LEU A 432 -71.15 -42.16 REMARK 500 ARG A 433 -61.33 -135.72 REMARK 500 LYS A 440 -8.80 82.69 REMARK 500 LEU B 4 -82.94 -58.97 REMARK 500 SER B 5 -4.11 52.08 REMARK 500 ILE B 29 -10.55 66.87 REMARK 500 ARG B 30 15.15 58.28 REMARK 500 ASN B 31 -12.07 58.87 REMARK 500 PRO B 40 -179.22 -60.77 REMARK 500 SER B 60 -127.09 47.75 REMARK 500 PRO B 140 44.79 -79.44 REMARK 500 GLU B 141 -60.28 -139.30 REMARK 500 LEU B 152 -70.92 -56.37 REMARK 500 SER B 188 59.26 -140.78 REMARK 500 LEU B 225 -60.98 -130.09 REMARK 500 TYR B 227 -77.87 -81.57 REMARK 500 SER B 228 70.55 58.91 REMARK 500 ARG B 230 -15.08 80.64 REMARK 500 GLN B 250 -70.46 -46.17 REMARK 500 LEU B 259 159.52 175.61 REMARK 500 THR B 303 -11.62 73.53 REMARK 500 ARG B 306 -73.16 -54.40 REMARK 500 LEU B 325 -65.41 -124.15 REMARK 500 HIS B 328 -72.10 -49.33 REMARK 500 GLN B 375 -121.74 43.07 REMARK 500 ALA B 421 -7.68 -59.14 REMARK 500 ARG B 422 -70.87 -46.14 REMARK 500 LEU B 425 -70.23 -52.83 REMARK 500 ALA B 431 -73.75 -57.05 REMARK 500 ARG B 433 -67.21 -134.55 REMARK 500 LEU B 439 -75.14 -57.49 REMARK 500 LYS B 440 -130.37 41.56 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 LEU A 3 LEU A 4 145.83 REMARK 500 ALA A 400 GLY A 401 -145.84 REMARK 500 SER A 417 TYR A 418 143.40 REMARK 500 SER B 8 ILE B 9 -148.63 REMARK 500 GLU B 374 GLN B 375 141.36 REMARK 500 ALA B 400 GLY B 401 -145.18 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 452 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 51 OD1 REMARK 620 2 ASP A 126 OD1 80.2 REMARK 620 3 ASP A 126 OD2 82.4 61.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 452 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 51 OD1 REMARK 620 2 ASP B 126 OD2 86.2 REMARK 620 N 1 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 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 453 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D5M B 453 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TAI RELATED DB: PDB REMARK 900 SAME PROTEIN OF APO FORM REMARK 900 RELATED ID: 3TAL RELATED DB: PDB REMARK 900 SAME PROTEIN OF MN-BOUND FORM DBREF 3TAZ A 1 451 UNP Q8U1N8 Q8U1N8_PYRFU 1 451 DBREF 3TAZ B 1 451 UNP Q8U1N8 Q8U1N8_PYRFU 1 451 SEQADV 3TAZ MET A -19 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ GLY A -18 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER A -17 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER A -16 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS A -15 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS A -14 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS A -13 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS A -12 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS A -11 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS A -10 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER A -9 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER A -8 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ GLY A -7 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ LEU A -6 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ VAL A -5 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ PRO A -4 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ ARG A -3 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ GLY A -2 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER A -1 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS A 0 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ MET B -19 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ GLY B -18 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER B -17 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER B -16 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS B -15 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS B -14 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS B -13 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS B -12 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS B -11 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS B -10 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER B -9 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER B -8 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ GLY B -7 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ LEU B -6 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ VAL B -5 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ PRO B -4 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ ARG B -3 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ GLY B -2 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ SER B -1 UNP Q8U1N8 EXPRESSION TAG SEQADV 3TAZ HIS B 0 UNP Q8U1N8 EXPRESSION TAG SEQRES 1 A 471 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 471 LEU VAL PRO ARG GLY SER HIS MET ARG LEU LEU SER LYS SEQRES 3 A 471 GLN SER ILE GLU ARG ILE THR LYS ILE LEU LEU ASP GLU SEQRES 4 A 471 LEU GLU ASN VAL ARG GLU ASN GLU GLN ILE ARG ASN ILE SEQRES 5 A 471 ILE ASN SER TRP LYS PRO LEU PRO SER PRO GLU LYS SER SEQRES 6 A 471 SER ILE TYR ALA VAL ASP GLY SER ARG SER VAL SER ARG SEQRES 7 A 471 LEU SER GLY THR VAL ILE TYR PHE LEU SER ALA LEU ALA SEQRES 8 A 471 VAL GLY SER GLY LYS GLN LEU ARG LEU SER TYR ALA ASN SEQRES 9 A 471 ALA ILE LYS SER ASN TYR GLY THR SER ASP GLN ILE VAL SEQRES 10 A 471 ARG MET GLN MET GLU THR LEU GLU ASN MET LEU GLY TYR SEQRES 11 A 471 LEU ALA TYR ARG LYS LEU GLU GLY GLU LYS ARG ALA ILE SEQRES 12 A 471 LEU MET ASP GLY THR LEU THR GLY SER LEU VAL ARG PRO SEQRES 13 A 471 PRO VAL TYR PRO GLU ASP ILE ARG SER LEU ASN VAL MET SEQRES 14 A 471 ARG ALA LEU ILE GLY GLU SER ASP PHE GLU ASN LEU LEU SEQRES 15 A 471 ASN GLU PHE LEU GLU LYS LEU ARG ASP HIS TYR ARG LYS SEQRES 16 A 471 VAL GLU GLU HIS LEU GLU LYS ASN GLY ASN TYR ASP SER SEQRES 17 A 471 PRO ILE LEU THR ASP ASN VAL VAL GLU LYS LEU ARG LYS SEQRES 18 A 471 LYS TYR ILE ASP THR LYS VAL ILE ALA TYR GLY SER GLY SEQRES 19 A 471 LYS VAL LYS VAL LYS ILE PRO ARG LYS ALA LEU GLY TYR SEQRES 20 A 471 SER PRO ARG VAL ILE PRO ILE GLU VAL LEU GLU SER SER SEQRES 21 A 471 ARG GLY LYS SER VAL ASP GLU LEU LEU GLN GLU LEU ASP SEQRES 22 A 471 GLU GLU LYS VAL GLU LEU TYR LEU GLY LYS ASP ASP ILE SEQRES 23 A 471 TYR ASP ALA LEU HIS MET THR LEU SER TYR ILE GLU TYR SEQRES 24 A 471 LEU TYR SER ILE ASP LYS LEU LEU GLU VAL LYS ASN LEU SEQRES 25 A 471 ALA TYR ILE ALA LYS SER PHE TYR THR LYS THR LEU ALA SEQRES 26 A 471 ARG THR LEU GLY VAL GLU ILE VAL ASP THR ALA LEU LEU SEQRES 27 A 471 ASP ALA VAL ILE ARG THR LEU ILE GLY HIS GLU LYS GLU SEQRES 28 A 471 GLY TYR LEU GLU ILE GLU HIS ALA VAL VAL PRO PRO LYS SEQRES 29 A 471 TRP SER PHE PRO ASP PHE LEU LEU SER LYS PHE ARG ASN SEQRES 30 A 471 ILE GLU LYS LEU ILE ASP LYS GLY ILE HIS LEU ALA TYR SEQRES 31 A 471 VAL ARG PHE GLU GLN GLY ASP VAL ILE TYR MET LEU GLN SEQRES 32 A 471 SER THR THR ASN ILE GLU LYS ILE LEU PRO LEU ILE LEU SEQRES 33 A 471 HIS HIS LYS ALA GLY GLY TYR LEU ARG PRO LEU GLN LEU SEQRES 34 A 471 ALA HIS HIS GLY VAL LYS ILE SER TYR LYS GLU ALA ARG SEQRES 35 A 471 HIS THR LEU GLU ALA LEU ILE ASN ALA LEU ARG ASN ARG SEQRES 36 A 471 ASP PRO ALA LEU LYS ILE PHE VAL LYS TYR GLY ARG SER SEQRES 37 A 471 PRO LEU GLU SEQRES 1 B 471 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 471 LEU VAL PRO ARG GLY SER HIS MET ARG LEU LEU SER LYS SEQRES 3 B 471 GLN SER ILE GLU ARG ILE THR LYS ILE LEU LEU ASP GLU SEQRES 4 B 471 LEU GLU ASN VAL ARG GLU ASN GLU GLN ILE ARG ASN ILE SEQRES 5 B 471 ILE ASN SER TRP LYS PRO LEU PRO SER PRO GLU LYS SER SEQRES 6 B 471 SER ILE TYR ALA VAL ASP GLY SER ARG SER VAL SER ARG SEQRES 7 B 471 LEU SER GLY THR VAL ILE TYR PHE LEU SER ALA LEU ALA SEQRES 8 B 471 VAL GLY SER GLY LYS GLN LEU ARG LEU SER TYR ALA ASN SEQRES 9 B 471 ALA ILE LYS SER ASN TYR GLY THR SER ASP GLN ILE VAL SEQRES 10 B 471 ARG MET GLN MET GLU THR LEU GLU ASN MET LEU GLY TYR SEQRES 11 B 471 LEU ALA TYR ARG LYS LEU GLU GLY GLU LYS ARG ALA ILE SEQRES 12 B 471 LEU MET ASP GLY THR LEU THR GLY SER LEU VAL ARG PRO SEQRES 13 B 471 PRO VAL TYR PRO GLU ASP ILE ARG SER LEU ASN VAL MET SEQRES 14 B 471 ARG ALA LEU ILE GLY GLU SER ASP PHE GLU ASN LEU LEU SEQRES 15 B 471 ASN GLU PHE LEU GLU LYS LEU ARG ASP HIS TYR ARG LYS SEQRES 16 B 471 VAL GLU GLU HIS LEU GLU LYS ASN GLY ASN TYR ASP SER SEQRES 17 B 471 PRO ILE LEU THR ASP ASN VAL VAL GLU LYS LEU ARG LYS SEQRES 18 B 471 LYS TYR ILE ASP THR LYS VAL ILE ALA TYR GLY SER GLY SEQRES 19 B 471 LYS VAL LYS VAL LYS ILE PRO ARG LYS ALA LEU GLY TYR SEQRES 20 B 471 SER PRO ARG VAL ILE PRO ILE GLU VAL LEU GLU SER SER SEQRES 21 B 471 ARG GLY LYS SER VAL ASP GLU LEU LEU GLN GLU LEU ASP SEQRES 22 B 471 GLU GLU LYS VAL GLU LEU TYR LEU GLY LYS ASP ASP ILE SEQRES 23 B 471 TYR ASP ALA LEU HIS MET THR LEU SER TYR ILE GLU TYR SEQRES 24 B 471 LEU TYR SER ILE ASP LYS LEU LEU GLU VAL LYS ASN LEU SEQRES 25 B 471 ALA TYR ILE ALA LYS SER PHE TYR THR LYS THR LEU ALA SEQRES 26 B 471 ARG THR LEU GLY VAL GLU ILE VAL ASP THR ALA LEU LEU SEQRES 27 B 471 ASP ALA VAL ILE ARG THR LEU ILE GLY HIS GLU LYS GLU SEQRES 28 B 471 GLY TYR LEU GLU ILE GLU HIS ALA VAL VAL PRO PRO LYS SEQRES 29 B 471 TRP SER PHE PRO ASP PHE LEU LEU SER LYS PHE ARG ASN SEQRES 30 B 471 ILE GLU LYS LEU ILE ASP LYS GLY ILE HIS LEU ALA TYR SEQRES 31 B 471 VAL ARG PHE GLU GLN GLY ASP VAL ILE TYR MET LEU GLN SEQRES 32 B 471 SER THR THR ASN ILE GLU LYS ILE LEU PRO LEU ILE LEU SEQRES 33 B 471 HIS HIS LYS ALA GLY GLY TYR LEU ARG PRO LEU GLN LEU SEQRES 34 B 471 ALA HIS HIS GLY VAL LYS ILE SER TYR LYS GLU ALA ARG SEQRES 35 B 471 HIS THR LEU GLU ALA LEU ILE ASN ALA LEU ARG ASN ARG SEQRES 36 B 471 ASP PRO ALA LEU LYS ILE PHE VAL LYS TYR GLY ARG SER SEQRES 37 B 471 PRO LEU GLU HET MN A 452 1 HET GOL A 453 6 HET MN B 452 1 HET D5M B 453 22 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN 2(MN 2+) FORMUL 4 GOL C3 H8 O3 FORMUL 6 D5M C10 H14 N5 O6 P FORMUL 7 HOH *9(H2 O) HELIX 1 1 LYS A 6 ARG A 24 1 19 HELIX 2 2 ILE A 32 TRP A 36 5 5 HELIX 3 3 ASN A 89 LYS A 115 1 27 HELIX 4 4 THR A 128 ARG A 135 1 8 HELIX 5 5 PRO A 140 ILE A 153 1 14 HELIX 6 6 GLY A 154 GLY A 184 1 31 HELIX 7 7 LEU A 191 ILE A 204 1 14 HELIX 8 8 ILE A 234 SER A 240 1 7 HELIX 9 9 SER A 244 GLU A 254 1 11 HELIX 10 10 GLY A 262 LEU A 287 1 26 HELIX 11 11 LYS A 302 THR A 307 1 6 HELIX 12 12 ASP A 314 THR A 324 1 11 HELIX 13 13 PRO A 343 PHE A 347 5 5 HELIX 14 14 PRO A 348 SER A 353 1 6 HELIX 15 15 PHE A 355 GLY A 365 1 11 HELIX 16 16 ASN A 387 HIS A 397 1 11 HELIX 17 17 LEU A 404 LYS A 415 1 12 HELIX 18 18 THR A 424 ARG A 433 1 10 HELIX 19 19 ASP A 436 LYS A 440 5 5 HELIX 20 20 SER B 5 GLU B 21 1 17 HELIX 21 21 ASN B 22 GLU B 27 1 6 HELIX 22 22 GLN B 28 SER B 35 5 8 HELIX 23 23 ASN B 89 LYS B 115 1 27 HELIX 24 24 THR B 128 ARG B 135 1 8 HELIX 25 25 VAL B 138 GLY B 154 1 17 HELIX 26 26 GLY B 154 ASN B 183 1 30 HELIX 27 27 LEU B 191 VAL B 208 1 18 HELIX 28 28 LYS B 223 LEU B 225 5 3 HELIX 29 29 ILE B 234 SER B 240 1 7 HELIX 30 30 SER B 244 GLU B 255 1 12 HELIX 31 31 GLY B 262 GLU B 288 1 27 HELIX 32 32 ASP B 314 ILE B 326 1 13 HELIX 33 33 PRO B 348 SER B 353 1 6 HELIX 34 34 PHE B 355 GLY B 365 1 11 HELIX 35 35 ASN B 387 HIS B 397 1 11 HELIX 36 36 LEU B 404 LYS B 415 1 12 HELIX 37 37 LYS B 419 ARG B 433 1 15 HELIX 38 38 ASN B 434 LYS B 440 1 7 SHEET 1 A 9 ASN A 185 TYR A 186 0 SHEET 2 A 9 LEU A 78 LYS A 87 1 N SER A 81 O TYR A 186 SHEET 3 A 9 THR A 62 GLY A 73 -1 N LEU A 67 O TYR A 82 SHEET 4 A 9 SER A 46 LEU A 59 -1 N LEU A 59 O THR A 62 SHEET 5 A 9 ARG A 121 MET A 125 1 O LEU A 124 N VAL A 50 SHEET 6 A 9 LEU A 292 ALA A 296 1 O ALA A 293 N MET A 125 SHEET 7 A 9 TYR A 380 SER A 384 -1 O MET A 381 N ALA A 296 SHEET 8 A 9 HIS A 367 ARG A 372 -1 N ALA A 369 O LEU A 382 SHEET 9 A 9 GLY A 332 GLU A 335 -1 N GLY A 332 O ARG A 372 SHEET 1 B 3 VAL A 208 TYR A 211 0 SHEET 2 B 3 LYS A 215 LYS A 219 -1 O LYS A 217 N ILE A 209 SHEET 3 B 3 GLU A 258 LEU A 259 -1 O LEU A 259 N VAL A 218 SHEET 1 C 2 ILE A 232 PRO A 233 0 SHEET 2 C 2 VAL B 231 ILE B 232 -1 O ILE B 232 N ILE A 232 SHEET 1 D 9 ASN B 185 TYR B 186 0 SHEET 2 D 9 LEU B 78 LYS B 87 1 N SER B 81 O TYR B 186 SHEET 3 D 9 THR B 62 GLY B 73 -1 N VAL B 63 O ILE B 86 SHEET 4 D 9 SER B 46 LEU B 59 -1 N SER B 57 O ILE B 64 SHEET 5 D 9 ARG B 121 MET B 125 1 O LEU B 124 N TYR B 48 SHEET 6 D 9 LEU B 292 ALA B 296 1 O ALA B 293 N ILE B 123 SHEET 7 D 9 ILE B 379 SER B 384 -1 O MET B 381 N ALA B 296 SHEET 8 D 9 HIS B 367 ARG B 372 -1 N ALA B 369 O LEU B 382 SHEET 9 D 9 GLY B 332 GLU B 335 -1 N GLY B 332 O ARG B 372 SHEET 1 E 2 LYS B 217 PRO B 221 0 SHEET 2 E 2 LYS B 256 TYR B 260 -1 O VAL B 257 N ILE B 220 LINK OD1 ASP A 51 MN MN A 452 1555 1555 2.21 LINK OD1 ASP A 126 MN MN A 452 1555 1555 2.20 LINK OD2 ASP A 126 MN MN A 452 1555 1555 2.20 LINK OD1 ASP B 51 MN MN B 452 1555 1555 2.21 LINK OD2 ASP B 126 MN MN B 452 1555 1555 2.21 CISPEP 1 TYR A 139 PRO A 140 0 3.90 CISPEP 2 GLY B 226 TYR B 227 0 15.37 CISPEP 3 SER B 228 PRO B 229 0 -7.36 CISPEP 4 PRO B 229 ARG B 230 0 20.02 SITE 1 AC1 4 ASP A 51 GLY A 52 GLU A 105 ASP A 126 SITE 1 AC2 4 SER A 74 SER A 239 HIS A 397 HIS A 398 SITE 1 AC3 2 ASP B 51 ASP B 126 SITE 1 AC4 10 ARG B 98 GLU B 102 GLY B 127 THR B 128 SITE 2 AC4 10 GLY B 131 SER B 132 ARG B 135 PRO B 137 SITE 3 AC4 10 PHE B 299 HOH B 454 CRYST1 65.158 114.847 123.414 90.00 90.00 90.00 P 21 21 21 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 0.015347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008103 0.00000