HEADER HYDROLASE 18-JUN-10 2XHQ OBSLTE 27-JUN-12 2XHQ 4AXQ TITLE CRYSTAL STRUCTURE OF ARCHAEMETZINCIN (AMZA) FROM ARCHAEOGLOBUS TITLE 2 FULGIDUS AT 1.45 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARCHAEMETZINCIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.-.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 2234; SOURCE 4 ATCC: 49558; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 11 OTHER_DETAILS: DSM 4304 KEYWDS METALLOPROTEASE, HYDROLASE, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.GRAEF,M.SCHACHERL,U.BAUMANN REVDAT 2 27-JUN-12 2XHQ 1 OBSLTE REVDAT 1 06-JUL-11 2XHQ 0 JRNL AUTH C.GRAEF,M.SCHACHERL,U.BAUMANN JRNL TITL CRYSTAL STRUCTURE OF ARCHAEMETZINCIN (AMZA) FROM JRNL TITL 2 ARCHAEOGLOBUS FULGIDUS AT 1.45 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.409 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.36 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.84 REMARK 3 NUMBER OF REFLECTIONS : 34388 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1688 REMARK 3 R VALUE (WORKING SET) : 0.1667 REMARK 3 FREE R VALUE : 0.2055 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.3 REMARK 3 FREE R VALUE TEST SET COUNT : 1825 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 25.4127 - 3.1222 1.00 3332 192 0.1776 0.1993 REMARK 3 2 3.1222 - 2.4789 1.00 3269 184 0.1753 0.2136 REMARK 3 3 2.4789 - 2.1657 1.00 3250 183 0.1550 0.2059 REMARK 3 4 2.1657 - 1.9678 1.00 3268 180 0.1467 0.1746 REMARK 3 5 1.9678 - 1.8268 1.00 3252 178 0.1469 0.1883 REMARK 3 6 1.8268 - 1.7191 1.00 3244 185 0.1538 0.2104 REMARK 3 7 1.7191 - 1.6330 1.00 3206 181 0.1542 0.2181 REMARK 3 8 1.6330 - 1.5620 1.00 3247 183 0.1547 0.2166 REMARK 3 9 1.5620 - 1.5018 1.00 3247 177 0.1587 0.2376 REMARK 3 10 1.5018 - 1.4500 1.00 3248 182 0.1691 0.2208 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 : 0.391 REMARK 3 B_SOL : 45.537 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.16 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.2678 REMARK 3 B22 (A**2) : -0.2678 REMARK 3 B33 (A**2) : 0.5356 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1346 REMARK 3 ANGLE : 1.209 1830 REMARK 3 CHIRALITY : 0.073 210 REMARK 3 PLANARITY : 0.005 234 REMARK 3 DIHEDRAL : 13.866 504 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 2XHQ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUN-10. REMARK 100 THE PDBE ID CODE IS EBI-44241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (MX-225) REMARK 200 DETECTOR MANUFACTURER : RAYONIX REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38203 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.40 REMARK 200 RESOLUTION RANGE LOW (A) : 25.40 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.2 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.77 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.80 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.99 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2X7M REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.5 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2 M (NH4)2SO4, REMARK 280 0.1 M HEPES PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.16950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.16950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.13750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.16950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.16950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.13750 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 44.16950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 44.16950 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.13750 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 44.16950 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 44.16950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.13750 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 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 A1161 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A -3 O REMARK 620 2 HIS A 117 NE2 169.9 REMARK 620 3 HIS A 121 NE2 96.6 90.7 REMARK 620 4 HIS A 127 NE2 86.0 100.5 94.6 REMARK 620 5 HOH A2253 O 88.4 84.1 174.8 87.3 REMARK 620 6 GLY A -3 N 79.8 92.3 97.4 162.4 82.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1162 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 151 SG REMARK 620 2 CYS A 154 SG 109.5 REMARK 620 3 CYS A 128 SG 105.1 111.6 REMARK 620 4 CYS A 132 SG 111.5 105.6 113.5 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 A1161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1162 DBREF 2XHQ A 1 160 UNP O29917 AMZA_ARCFU 1 160 SEQADV 2XHQ GLY A -3 UNP O29917 EXPRESSION TAG SEQADV 2XHQ SER A -2 UNP O29917 EXPRESSION TAG SEQADV 2XHQ HIS A -1 UNP O29917 EXPRESSION TAG SEQRES 1 A 163 GLY SER HIS MET LYS ILE TYR ILE GLN PRO LEU SER VAL SEQRES 2 A 163 ASN SER HIS THR VAL GLU VAL LEU ALA ASN SER LEU PRO SEQRES 3 A 163 LYS ILE PHE ASN ALA GLU VAL PHE VAL LEU PRO ALA SER SEQRES 4 A 163 ASP VAL SER LEU LYS CYS TYR ASN ALA SER ARG ARG GLN SEQRES 5 A 163 TYR ASN SER THR CYS ILE LEU ARG MET LEU PRO PRO ILE SEQRES 6 A 163 LYS VAL THR LEU GLY VAL THR GLY LYS ASP ILE TYR ALA SEQRES 7 A 163 LYS GLY MET ASN PHE VAL PHE GLY GLU ALA GLU LEU GLY SEQRES 8 A 163 GLY ALA ARG ALA VAL LEU SER VAL PHE ARG LEU THR THR SEQRES 9 A 163 ALA ASP SER GLU LEU TYR ARG GLU ARG VAL VAL LYS GLU SEQRES 10 A 163 ALA VAL HIS GLU ILE GLY HIS VAL LEU GLY LEU LYS HIS SEQRES 11 A 163 CYS SER ASN ASN CYS VAL MET ARG PHE SER ASN SER VAL SEQRES 12 A 163 GLN ASP VAL ASP ARG LYS PRO VAL SER PHE CYS ARG GLU SEQRES 13 A 163 CYS ALA SER LYS ILE ARG TYR HET ZN A1161 1 HET ZN A1162 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 3 HOH *253(H2 O) HELIX 1 1 ASN A 11 ASN A 27 1 17 HELIX 2 2 SER A 39 LYS A 41 5 3 HELIX 3 3 SER A 52 LEU A 59 1 8 HELIX 4 4 PHE A 97 THR A 100 5 4 HELIX 5 5 ASP A 103 LEU A 123 1 21 HELIX 6 6 SER A 139 LYS A 146 1 8 HELIX 7 7 CYS A 151 TYR A 160 1 10 SHEET 1 AA 5 ALA A 28 VAL A 32 0 SHEET 2 AA 5 MET A 1 LEU A 8 1 O MET A 1 N GLU A 29 SHEET 3 AA 5 THR A 65 THR A 69 1 O LEU A 66 N GLN A 6 SHEET 4 AA 5 ARG A 91 SER A 95 1 O ALA A 92 N GLY A 67 SHEET 5 AA 5 GLY A 83 ALA A 85 -1 O GLU A 84 N VAL A 93 SHEET 1 AB 3 TYR A 43 ASN A 44 0 SHEET 2 AB 3 GLN A 49 ASN A 51 -1 O GLN A 49 N ASN A 44 SHEET 3 AB 3 ILE A 73 TYR A 74 1 N TYR A 74 O TYR A 50 SSBOND 1 CYS A 42 CYS A 54 1555 1555 2.03 LINK ZN ZN A1161 O GLY A -3 1555 6454 2.12 LINK ZN ZN A1161 NE2 HIS A 117 1555 1555 2.10 LINK ZN ZN A1161 NE2 HIS A 121 1555 1555 2.16 LINK ZN ZN A1161 NE2 HIS A 127 1555 1555 2.05 LINK ZN ZN A1161 O HOH A2253 1555 1555 2.20 LINK ZN ZN A1161 N GLY A -3 1555 6454 2.18 LINK ZN ZN A1162 SG CYS A 154 1555 1555 2.32 LINK ZN ZN A1162 SG CYS A 128 1555 1555 2.32 LINK ZN ZN A1162 SG CYS A 132 1555 1555 2.33 LINK ZN ZN A1162 SG CYS A 151 1555 1555 2.36 CISPEP 1 LYS A 63 VAL A 64 0 -8.93 SITE 1 AC1 5 GLY A -3 HIS A 117 HIS A 121 HIS A 127 SITE 2 AC1 5 HOH A2253 SITE 1 AC2 4 CYS A 128 CYS A 132 CYS A 151 CYS A 154 CRYST1 88.339 88.339 50.275 90.00 90.00 90.00 I 4 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 0.011320 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019891 0.00000