HEADER OXIDOREDUCTASE 01-OCT-10 3P2A TITLE CRYSTAL STRUCTURE OF THIOREDOXIN 2 FROM YERSINIA PESTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE THIOREDOXIN-LIKE PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: THIOREDOXIN 2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 214092; SOURCE 4 STRAIN: CO92; SOURCE 5 GENE: TRXC, Y0919, YPO3270, YP_0661; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 2 DISEASES, CSGID, ALPHA-BETA-ALPHA SANDWICH, ENERGY METABOLISM, KEYWDS 3 CYTOSOL, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,M.ZHOU,S.GRIMSHAW,W.F.ANDERSON,A.JOACHIMIAK,CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 1 13-OCT-10 3P2A 0 JRNL AUTH Y.KIM,M.ZHOU,S.GRIMSHAW,W.F.ANDERSON,A.JOACHIMIAK, JRNL AUTH 2 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES JRNL AUTH 3 (CSGID) JRNL TITL CRYSTAL STRUCTURE OF THIOREDOXIN 2 FROM YERSINIA PESTIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 33249 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1692 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 34.2889 - 4.7252 0.99 3221 185 0.1448 0.1552 REMARK 3 2 4.7252 - 3.7520 1.00 3186 189 0.1400 0.1978 REMARK 3 3 3.7520 - 3.2782 1.00 3172 171 0.1922 0.2283 REMARK 3 4 3.2782 - 2.9786 1.00 3200 155 0.1987 0.2650 REMARK 3 5 2.9786 - 2.7652 0.99 3170 171 0.2237 0.2937 REMARK 3 6 2.7652 - 2.6023 0.99 3166 152 0.2143 0.2984 REMARK 3 7 2.6023 - 2.4720 0.99 3138 181 0.2146 0.3119 REMARK 3 8 2.4720 - 2.3644 0.99 3124 151 0.2142 0.2844 REMARK 3 9 2.3644 - 2.2734 0.99 3144 177 0.2244 0.2791 REMARK 3 10 2.2734 - 2.1950 0.95 3036 160 0.2370 0.3283 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 27.87 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.11350 REMARK 3 B22 (A**2) : 3.53560 REMARK 3 B33 (A**2) : -6.64910 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.57810 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 : 0.014 4558 REMARK 3 ANGLE : 1.564 6172 REMARK 3 CHIRALITY : 0.100 681 REMARK 3 PLANARITY : 0.008 816 REMARK 3 DIHEDRAL : 16.643 1707 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 63.1071 -2.9317 28.2322 REMARK 3 T TENSOR REMARK 3 T11: 0.0145 T22: 0.0698 REMARK 3 T33: 0.0591 T12: -0.0069 REMARK 3 T13: -0.0042 T23: -0.0362 REMARK 3 L TENSOR REMARK 3 L11: 0.4576 L22: 1.0705 REMARK 3 L33: 1.2000 L12: -0.0008 REMARK 3 L13: -0.2842 L23: -0.6555 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: 0.0401 S13: -0.0292 REMARK 3 S21: 0.0888 S22: 0.0247 S23: -0.0694 REMARK 3 S31: -0.0561 S32: -0.0152 S33: -0.0355 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 36.1499 8.6458 10.6211 REMARK 3 T TENSOR REMARK 3 T11: 0.1558 T22: 0.2374 REMARK 3 T33: 0.1647 T12: -0.0361 REMARK 3 T13: 0.0063 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.0967 L22: 1.1074 REMARK 3 L33: 1.0269 L12: 0.1082 REMARK 3 L13: 0.2455 L23: 0.3170 REMARK 3 S TENSOR REMARK 3 S11: -0.0090 S12: 0.1570 S13: -0.0144 REMARK 3 S21: -0.1734 S22: 0.0157 S23: -0.0120 REMARK 3 S31: -0.0473 S32: 0.1236 S33: -0.0095 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 42.5635 35.5205 8.1020 REMARK 3 T TENSOR REMARK 3 T11: 0.3669 T22: 0.2928 REMARK 3 T33: 0.1355 T12: -0.1160 REMARK 3 T13: 0.0016 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 2.1798 L22: 2.2142 REMARK 3 L33: 1.2496 L12: 0.6605 REMARK 3 L13: -1.6017 L23: -0.7456 REMARK 3 S TENSOR REMARK 3 S11: 0.2693 S12: -0.5370 S13: 0.0316 REMARK 3 S21: 0.6424 S22: -0.2535 S23: 0.0423 REMARK 3 S31: -0.3537 S32: 0.3762 S33: -0.0199 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 37.9210 8.0367 46.9249 REMARK 3 T TENSOR REMARK 3 T11: 0.2086 T22: 0.1516 REMARK 3 T33: 0.1627 T12: -0.0539 REMARK 3 T13: 0.0211 T23: 0.0247 REMARK 3 L TENSOR REMARK 3 L11: 0.7990 L22: 1.5936 REMARK 3 L33: 1.5821 L12: 0.4359 REMARK 3 L13: 0.5966 L23: 0.9765 REMARK 3 S TENSOR REMARK 3 S11: 0.0819 S12: -0.1642 S13: 0.0274 REMARK 3 S21: 0.3206 S22: -0.0509 S23: 0.0145 REMARK 3 S31: 0.3524 S32: -0.1683 S33: -0.0222 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 3P2A COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-10. REMARK 100 THE RCSB ID CODE IS RCSB061866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-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 : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97923 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33346 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13100 REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.77700 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL3000, SHELXS,MLPHARE,RESOLVE,SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH REMARK 280 7.5, 25 % W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 37.79100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 107.94000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -37.79100 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 6 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 SER A -2 REMARK 465 ASN A 144 REMARK 465 SER A 145 REMARK 465 SER B -2 REMARK 465 PRO B 143 REMARK 465 ASN B 144 REMARK 465 SER B 145 REMARK 465 SER C -2 REMARK 465 ASN C -1 REMARK 465 ALA C 0 REMARK 465 ASP C 142 REMARK 465 PRO C 143 REMARK 465 ASN C 144 REMARK 465 SER C 145 REMARK 465 SER D -2 REMARK 465 ASN D -1 REMARK 465 ASP D 142 REMARK 465 PRO D 143 REMARK 465 ASN D 144 REMARK 465 SER D 145 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 MSE B 9 3.93 83.87 REMARK 500 ALA B 82 -39.81 -39.07 REMARK 500 ARG B 141 154.36 -46.50 REMARK 500 MSE C 9 -5.23 68.62 REMARK 500 ASP C 20 -176.33 -171.29 REMARK 500 ALA C 23 124.45 -38.18 REMARK 500 ASP C 51 151.16 -47.87 REMARK 500 LYS C 84 -35.31 -134.19 REMARK 500 ASN C 123 62.68 -101.82 REMARK 500 MSE D 1 141.34 175.25 REMARK 500 ASP D 51 152.91 -44.53 REMARK 500 ALA D 82 -37.71 -34.15 REMARK 500 MSE D 121 136.65 -170.11 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 B 254 DISTANCE = 5.76 ANGSTROMS 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 ZN D 151 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 8 SG REMARK 620 2 CYS D 28 SG 112.4 REMARK 620 3 CYS D 5 SG 114.9 108.4 REMARK 620 4 CYS D 25 SG 106.5 111.1 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 151 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 25 SG REMARK 620 2 CYS A 8 SG 108.6 REMARK 620 3 CYS A 5 SG 107.7 116.0 REMARK 620 4 CYS A 28 SG 113.1 109.7 101.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 151 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 28 SG REMARK 620 2 CYS B 25 SG 115.7 REMARK 620 3 CYS B 8 SG 109.0 107.2 REMARK 620 4 CYS B 5 SG 104.1 108.6 112.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 151 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 5 SG REMARK 620 2 CYS C 8 SG 112.9 REMARK 620 3 CYS C 25 SG 102.1 111.4 REMARK 620 4 CYS C 28 SG 110.2 106.3 114.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 151 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP04482 RELATED DB: TARGETDB DBREF 3P2A A 1 145 UNP Q7CK81 Q7CK81_YERPE 1 145 DBREF 3P2A B 1 145 UNP Q7CK81 Q7CK81_YERPE 1 145 DBREF 3P2A C 1 145 UNP Q7CK81 Q7CK81_YERPE 1 145 DBREF 3P2A D 1 145 UNP Q7CK81 Q7CK81_YERPE 1 145 SEQADV 3P2A SER A -2 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ASN A -1 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ALA A 0 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A SER B -2 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ASN B -1 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ALA B 0 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A SER C -2 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ASN C -1 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ALA C 0 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A SER D -2 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ASN D -1 UNP Q7CK81 EXPRESSION TAG SEQADV 3P2A ALA D 0 UNP Q7CK81 EXPRESSION TAG SEQRES 1 A 148 SER ASN ALA MSE ASN THR VAL CYS THR ALA CYS MSE ALA SEQRES 2 A 148 THR ASN ARG LEU PRO GLU GLU ARG ILE ASP ASP GLY ALA SEQRES 3 A 148 LYS CYS GLY ARG CYS GLY HIS SER LEU PHE ASP GLY GLU SEQRES 4 A 148 VAL ILE ASN ALA THR ALA GLU THR LEU ASP LYS LEU LEU SEQRES 5 A 148 GLN ASP ASP LEU PRO MSE VAL ILE ASP PHE TRP ALA PRO SEQRES 6 A 148 TRP CYS GLY PRO CYS ARG SER PHE ALA PRO ILE PHE ALA SEQRES 7 A 148 GLU THR ALA ALA GLU ARG ALA GLY LYS VAL ARG PHE VAL SEQRES 8 A 148 LYS VAL ASN THR GLU ALA GLU PRO ALA LEU SER THR ARG SEQRES 9 A 148 PHE ARG ILE ARG SER ILE PRO THR ILE MSE LEU TYR ARG SEQRES 10 A 148 ASN GLY LYS MSE ILE ASP MSE LEU ASN GLY ALA VAL PRO SEQRES 11 A 148 LYS ALA PRO PHE ASP ASN TRP LEU ASP GLU GLN LEU SER SEQRES 12 A 148 ARG ASP PRO ASN SER SEQRES 1 B 148 SER ASN ALA MSE ASN THR VAL CYS THR ALA CYS MSE ALA SEQRES 2 B 148 THR ASN ARG LEU PRO GLU GLU ARG ILE ASP ASP GLY ALA SEQRES 3 B 148 LYS CYS GLY ARG CYS GLY HIS SER LEU PHE ASP GLY GLU SEQRES 4 B 148 VAL ILE ASN ALA THR ALA GLU THR LEU ASP LYS LEU LEU SEQRES 5 B 148 GLN ASP ASP LEU PRO MSE VAL ILE ASP PHE TRP ALA PRO SEQRES 6 B 148 TRP CYS GLY PRO CYS ARG SER PHE ALA PRO ILE PHE ALA SEQRES 7 B 148 GLU THR ALA ALA GLU ARG ALA GLY LYS VAL ARG PHE VAL SEQRES 8 B 148 LYS VAL ASN THR GLU ALA GLU PRO ALA LEU SER THR ARG SEQRES 9 B 148 PHE ARG ILE ARG SER ILE PRO THR ILE MSE LEU TYR ARG SEQRES 10 B 148 ASN GLY LYS MSE ILE ASP MSE LEU ASN GLY ALA VAL PRO SEQRES 11 B 148 LYS ALA PRO PHE ASP ASN TRP LEU ASP GLU GLN LEU SER SEQRES 12 B 148 ARG ASP PRO ASN SER SEQRES 1 C 148 SER ASN ALA MSE ASN THR VAL CYS THR ALA CYS MSE ALA SEQRES 2 C 148 THR ASN ARG LEU PRO GLU GLU ARG ILE ASP ASP GLY ALA SEQRES 3 C 148 LYS CYS GLY ARG CYS GLY HIS SER LEU PHE ASP GLY GLU SEQRES 4 C 148 VAL ILE ASN ALA THR ALA GLU THR LEU ASP LYS LEU LEU SEQRES 5 C 148 GLN ASP ASP LEU PRO MSE VAL ILE ASP PHE TRP ALA PRO SEQRES 6 C 148 TRP CYS GLY PRO CYS ARG SER PHE ALA PRO ILE PHE ALA SEQRES 7 C 148 GLU THR ALA ALA GLU ARG ALA GLY LYS VAL ARG PHE VAL SEQRES 8 C 148 LYS VAL ASN THR GLU ALA GLU PRO ALA LEU SER THR ARG SEQRES 9 C 148 PHE ARG ILE ARG SER ILE PRO THR ILE MSE LEU TYR ARG SEQRES 10 C 148 ASN GLY LYS MSE ILE ASP MSE LEU ASN GLY ALA VAL PRO SEQRES 11 C 148 LYS ALA PRO PHE ASP ASN TRP LEU ASP GLU GLN LEU SER SEQRES 12 C 148 ARG ASP PRO ASN SER SEQRES 1 D 148 SER ASN ALA MSE ASN THR VAL CYS THR ALA CYS MSE ALA SEQRES 2 D 148 THR ASN ARG LEU PRO GLU GLU ARG ILE ASP ASP GLY ALA SEQRES 3 D 148 LYS CYS GLY ARG CYS GLY HIS SER LEU PHE ASP GLY GLU SEQRES 4 D 148 VAL ILE ASN ALA THR ALA GLU THR LEU ASP LYS LEU LEU SEQRES 5 D 148 GLN ASP ASP LEU PRO MSE VAL ILE ASP PHE TRP ALA PRO SEQRES 6 D 148 TRP CYS GLY PRO CYS ARG SER PHE ALA PRO ILE PHE ALA SEQRES 7 D 148 GLU THR ALA ALA GLU ARG ALA GLY LYS VAL ARG PHE VAL SEQRES 8 D 148 LYS VAL ASN THR GLU ALA GLU PRO ALA LEU SER THR ARG SEQRES 9 D 148 PHE ARG ILE ARG SER ILE PRO THR ILE MSE LEU TYR ARG SEQRES 10 D 148 ASN GLY LYS MSE ILE ASP MSE LEU ASN GLY ALA VAL PRO SEQRES 11 D 148 LYS ALA PRO PHE ASP ASN TRP LEU ASP GLU GLN LEU SER SEQRES 12 D 148 ARG ASP PRO ASN SER MODRES 3P2A MSE A 1 MET SELENOMETHIONINE MODRES 3P2A MSE A 9 MET SELENOMETHIONINE MODRES 3P2A MSE A 55 MET SELENOMETHIONINE MODRES 3P2A MSE A 111 MET SELENOMETHIONINE MODRES 3P2A MSE A 118 MET SELENOMETHIONINE MODRES 3P2A MSE A 121 MET SELENOMETHIONINE MODRES 3P2A MSE B 1 MET SELENOMETHIONINE MODRES 3P2A MSE B 9 MET SELENOMETHIONINE MODRES 3P2A MSE B 55 MET SELENOMETHIONINE MODRES 3P2A MSE B 111 MET SELENOMETHIONINE MODRES 3P2A MSE B 118 MET SELENOMETHIONINE MODRES 3P2A MSE B 121 MET SELENOMETHIONINE MODRES 3P2A MSE C 1 MET SELENOMETHIONINE MODRES 3P2A MSE C 9 MET SELENOMETHIONINE MODRES 3P2A MSE C 55 MET SELENOMETHIONINE MODRES 3P2A MSE C 111 MET SELENOMETHIONINE MODRES 3P2A MSE C 118 MET SELENOMETHIONINE MODRES 3P2A MSE C 121 MET SELENOMETHIONINE MODRES 3P2A MSE D 1 MET SELENOMETHIONINE MODRES 3P2A MSE D 9 MET SELENOMETHIONINE MODRES 3P2A MSE D 55 MET SELENOMETHIONINE MODRES 3P2A MSE D 111 MET SELENOMETHIONINE MODRES 3P2A MSE D 118 MET SELENOMETHIONINE MODRES 3P2A MSE D 121 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 9 8 HET MSE A 55 8 HET MSE A 111 8 HET MSE A 118 8 HET MSE A 121 8 HET MSE B 1 8 HET MSE B 9 8 HET MSE B 55 8 HET MSE B 111 8 HET MSE B 118 8 HET MSE B 121 8 HET MSE C 1 8 HET MSE C 9 8 HET MSE C 55 8 HET MSE C 111 8 HET MSE C 118 8 HET MSE C 121 8 HET MSE D 1 8 HET MSE D 9 8 HET MSE D 55 8 HET MSE D 111 8 HET MSE D 118 8 HET MSE D 121 8 HET ZN A 151 1 HET FMT A 152 3 HET ZN B 151 1 HET ZN C 151 1 HET ZN D 151 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID FORMUL 1 MSE 24(C5 H11 N O2 SE) FORMUL 5 ZN 4(ZN 2+) FORMUL 6 FMT C H2 O2 FORMUL 10 HOH *353(H2 O) HELIX 1 1 THR A 44 LEU A 49 1 6 HELIX 2 2 CYS A 64 ARG A 81 1 18 HELIX 3 3 GLU A 95 PHE A 102 1 8 HELIX 4 4 PRO A 127 ARG A 141 1 15 HELIX 5 5 THR B 44 LEU B 49 1 6 HELIX 6 6 CYS B 64 ARG B 81 1 18 HELIX 7 7 GLU B 95 PHE B 102 1 8 HELIX 8 8 PRO B 127 ARG B 141 1 15 HELIX 9 9 THR C 44 GLN C 50 1 7 HELIX 10 10 CYS C 64 ARG C 81 1 18 HELIX 11 11 GLU C 95 PHE C 102 1 8 HELIX 12 12 PRO C 127 LEU C 139 1 13 HELIX 13 13 THR D 44 GLN D 50 1 7 HELIX 14 14 CYS D 64 ARG D 81 1 18 HELIX 15 15 GLU D 95 PHE D 102 1 8 HELIX 16 16 PRO D 127 SER D 140 1 14 SHEET 1 A 2 ALA A 0 VAL A 4 0 SHEET 2 A 2 THR A 11 PRO A 15 -1 O ASN A 12 N THR A 3 SHEET 1 B 5 ILE A 38 ASN A 39 0 SHEET 2 B 5 ARG A 86 ASN A 91 1 O PHE A 87 N ILE A 38 SHEET 3 B 5 MSE A 55 TRP A 60 1 N VAL A 56 O VAL A 88 SHEET 4 B 5 THR A 109 ARG A 114 -1 O THR A 109 N PHE A 59 SHEET 5 B 5 LYS A 117 LEU A 122 -1 O ILE A 119 N LEU A 112 SHEET 1 C 2 ALA B 0 VAL B 4 0 SHEET 2 C 2 THR B 11 PRO B 15 -1 O ASN B 12 N THR B 3 SHEET 1 D 5 VAL B 37 ASN B 39 0 SHEET 2 D 5 ARG B 86 ASN B 91 1 O PHE B 87 N ILE B 38 SHEET 3 D 5 MSE B 55 TRP B 60 1 N VAL B 56 O VAL B 88 SHEET 4 D 5 THR B 109 ARG B 114 -1 O TYR B 113 N MSE B 55 SHEET 5 D 5 LYS B 117 ASN B 123 -1 O LEU B 122 N ILE B 110 SHEET 1 E 2 ASN C 2 VAL C 4 0 SHEET 2 E 2 THR C 11 ARG C 13 -1 O ASN C 12 N THR C 3 SHEET 1 F 5 VAL C 37 ASN C 39 0 SHEET 2 F 5 ARG C 86 ASN C 91 1 O LYS C 89 N ILE C 38 SHEET 3 F 5 MSE C 55 TRP C 60 1 N ASP C 58 O VAL C 88 SHEET 4 F 5 THR C 109 ARG C 114 -1 O TYR C 113 N MSE C 55 SHEET 5 F 5 LYS C 117 LEU C 122 -1 O ILE C 119 N LEU C 112 SHEET 1 G 2 MSE D 1 VAL D 4 0 SHEET 2 G 2 THR D 11 LEU D 14 -1 O ASN D 12 N THR D 3 SHEET 1 H 5 ILE D 38 ASN D 39 0 SHEET 2 H 5 ARG D 86 ASN D 91 1 O PHE D 87 N ILE D 38 SHEET 3 H 5 MSE D 55 TRP D 60 1 N ASP D 58 O VAL D 88 SHEET 4 H 5 THR D 109 ARG D 114 -1 O TYR D 113 N MSE D 55 SHEET 5 H 5 LYS D 117 LEU D 122 -1 O ILE D 119 N LEU D 112 SSBOND 1 CYS A 64 CYS A 67 1555 1555 2.10 SSBOND 2 CYS B 64 CYS B 67 1555 1555 2.10 SSBOND 3 CYS C 64 CYS C 67 1555 1555 2.10 SSBOND 4 CYS D 64 CYS D 67 1555 1555 2.11 LINK C ALA A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 LINK C CYS A 8 N MSE A 9 1555 1555 1.34 LINK C MSE A 9 N ALA A 10 1555 1555 1.32 LINK C PRO A 54 N MSE A 55 1555 1555 1.32 LINK C MSE A 55 N VAL A 56 1555 1555 1.33 LINK C ILE A 110 N MSE A 111 1555 1555 1.32 LINK C MSE A 111 N LEU A 112 1555 1555 1.33 LINK C LYS A 117 N MSE A 118 1555 1555 1.33 LINK C MSE A 118 N ILE A 119 1555 1555 1.32 LINK C ASP A 120 N MSE A 121 1555 1555 1.32 LINK C MSE A 121 N LEU A 122 1555 1555 1.33 LINK C ALA B 0 N MSE B 1 1555 1555 1.33 LINK C MSE B 1 N ASN B 2 1555 1555 1.34 LINK C CYS B 8 N MSE B 9 1555 1555 1.34 LINK C MSE B 9 N ALA B 10 1555 1555 1.32 LINK C PRO B 54 N MSE B 55 1555 1555 1.33 LINK C MSE B 55 N VAL B 56 1555 1555 1.32 LINK C ILE B 110 N MSE B 111 1555 1555 1.32 LINK C MSE B 111 N LEU B 112 1555 1555 1.33 LINK C LYS B 117 N MSE B 118 1555 1555 1.33 LINK C MSE B 118 N ILE B 119 1555 1555 1.33 LINK C ASP B 120 N MSE B 121 1555 1555 1.32 LINK C MSE B 121 N LEU B 122 1555 1555 1.32 LINK C MSE C 1 N ASN C 2 1555 1555 1.35 LINK C CYS C 8 N MSE C 9 1555 1555 1.33 LINK C MSE C 9 N ALA C 10 1555 1555 1.33 LINK C PRO C 54 N MSE C 55 1555 1555 1.31 LINK C MSE C 55 N VAL C 56 1555 1555 1.34 LINK C ILE C 110 N MSE C 111 1555 1555 1.32 LINK C MSE C 111 N LEU C 112 1555 1555 1.33 LINK C LYS C 117 N MSE C 118 1555 1555 1.32 LINK C MSE C 118 N ILE C 119 1555 1555 1.33 LINK C ASP C 120 N MSE C 121 1555 1555 1.33 LINK C MSE C 121 N LEU C 122 1555 1555 1.33 LINK C ALA D 0 N MSE D 1 1555 1555 1.34 LINK C MSE D 1 N ASN D 2 1555 1555 1.34 LINK C CYS D 8 N MSE D 9 1555 1555 1.34 LINK C MSE D 9 N ALA D 10 1555 1555 1.33 LINK C PRO D 54 N MSE D 55 1555 1555 1.32 LINK C MSE D 55 N VAL D 56 1555 1555 1.33 LINK C ILE D 110 N MSE D 111 1555 1555 1.33 LINK C MSE D 111 N LEU D 112 1555 1555 1.33 LINK C LYS D 117 N MSE D 118 1555 1555 1.33 LINK C MSE D 118 N ILE D 119 1555 1555 1.32 LINK C ASP D 120 N MSE D 121 1555 1555 1.32 LINK C MSE D 121 N LEU D 122 1555 1555 1.33 LINK SG CYS D 8 ZN ZN D 151 1555 1555 2.28 LINK SG CYS D 28 ZN ZN D 151 1555 1555 2.29 LINK SG CYS A 25 ZN ZN A 151 1555 1555 2.31 LINK SG CYS B 28 ZN ZN B 151 1555 1555 2.32 LINK SG CYS C 5 ZN ZN C 151 1555 1555 2.33 LINK SG CYS C 8 ZN ZN C 151 1555 1555 2.34 LINK SG CYS A 8 ZN ZN A 151 1555 1555 2.35 LINK SG CYS A 5 ZN ZN A 151 1555 1555 2.37 LINK SG CYS B 25 ZN ZN B 151 1555 1555 2.38 LINK SG CYS B 8 ZN ZN B 151 1555 1555 2.38 LINK SG CYS B 5 ZN ZN B 151 1555 1555 2.41 LINK SG CYS A 28 ZN ZN A 151 1555 1555 2.42 LINK SG CYS C 25 ZN ZN C 151 1555 1555 2.43 LINK SG CYS D 5 ZN ZN D 151 1555 1555 2.47 LINK SG CYS C 28 ZN ZN C 151 1555 1555 2.49 LINK SG CYS D 25 ZN ZN D 151 1555 1555 2.53 CISPEP 1 ILE A 107 PRO A 108 0 1.50 CISPEP 2 ILE B 107 PRO B 108 0 -1.16 CISPEP 3 ILE C 107 PRO C 108 0 -0.37 CISPEP 4 ILE D 107 PRO D 108 0 -2.97 SITE 1 AC1 4 CYS A 5 CYS A 8 CYS A 25 CYS A 28 SITE 1 AC2 1 LYS A 24 SITE 1 AC3 4 CYS B 5 CYS B 8 CYS B 25 CYS B 28 SITE 1 AC4 4 CYS C 5 CYS C 8 CYS C 25 CYS C 28 SITE 1 AC5 4 CYS D 5 CYS D 8 CYS D 25 CYS D 28 CRYST1 53.970 75.582 81.512 90.00 90.85 90.00 P 1 21 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 0.018529 0.000000 0.000275 0.00000 SCALE2 0.000000 0.013231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012269 0.00000