HEADER HYDROLASE 14-OCT-18 6IK4 TITLE A NOVEL M23 METALLOPROTEASE PSEUDOALTERIN FROM DEEP-SEA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELASTINOLYTIC METALLOPROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 231-403 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOALTEROMONAS SP. CF6-2; SOURCE 3 ORGANISM_TAXID: 562716 KEYWDS M23 FAMILY, ELASTASE, PEPTIDOGLYCAN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.L.ZHAO,B.L.TANG,J.YANG,X.L.CHEN,Y.Z.ZHANG REVDAT 3 22-NOV-23 6IK4 1 REMARK REVDAT 2 29-APR-20 6IK4 1 JRNL REVDAT 1 16-OCT-19 6IK4 0 JRNL AUTH B.L.TANG,J.YANG,X.L.CHEN,P.WANG,H.L.ZHAO,H.N.SU,C.Y.LI,Y.YU, JRNL AUTH 2 S.ZHONG,L.WANG,I.LIDBURY,H.DING,M.WANG,A.MCMINN,X.Y.ZHANG, JRNL AUTH 3 Y.CHEN,Y.Z.ZHANG JRNL TITL A PREDATOR-PREY INTERACTION BETWEEN A MARINE JRNL TITL 2 PSEUDOALTEROMONAS SP. AND GRAM-POSITIVE BACTERIA. JRNL REF NAT COMMUN V. 11 285 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 31941905 JRNL DOI 10.1038/S41467-019-14133-X REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15332 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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 41.3238 - 3.2493 1.00 3057 131 0.1446 0.1371 REMARK 3 2 3.2493 - 2.5791 1.00 2890 182 0.1539 0.1835 REMARK 3 3 2.5791 - 2.2532 1.00 2870 169 0.1546 0.1950 REMARK 3 4 2.2532 - 2.0472 1.00 2901 135 0.1465 0.2086 REMARK 3 5 2.0472 - 1.9004 0.99 2867 130 0.1478 0.1865 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.006 1435 REMARK 3 ANGLE : 0.901 1956 REMARK 3 CHIRALITY : 0.056 187 REMARK 3 PLANARITY : 0.005 261 REMARK 3 DIHEDRAL : 11.641 808 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 6IK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3IT5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS (PH 7.1), 0.6M MAGNESIUM REMARK 280 FORMATE DEHYDRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 36.70950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.70950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 31.42050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.22150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.42050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.22150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.70950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.42050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.22150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.70950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.42050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.22150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 70 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 PRO A 8 42.69 -79.73 REMARK 500 HIS A 79 37.97 73.53 REMARK 500 ASN A 139 -1.23 70.09 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 21 NE2 REMARK 620 2 ASP A 34 OD1 100.5 REMARK 620 3 HIS A 120 ND1 107.7 107.8 REMARK 620 4 GOL A 202 O2 87.1 143.7 103.3 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 DBREF 6IK4 A 1 173 UNP E7D102 E7D102_9GAMM 231 403 SEQRES 1 A 173 ALA THR PHE THR MET ASN LEU PRO TRP SER GLN GLY TYR SEQRES 2 A 173 TYR TRP TYR SER GLY GLY ALA HIS SER ASN THR GLY SER SEQRES 3 A 173 GLY TYR PRO TYR SER SER LEU ASP PHE ASN ASN GLY SER SEQRES 4 A 173 GLY GLY TRP GLY SER ASN THR PRO TRP VAL GLN ALA ALA SEQRES 5 A 173 HIS GLY GLY VAL ILE THR ARG PHE SER SER CYS ASN ILE SEQRES 6 A 173 ARG VAL THR HIS SER SER GLY PHE ALA THR ASN TYR TYR SEQRES 7 A 173 HIS MET SER ASN LEU GLN TYR ASN ASN GLY ASP THR VAL SEQRES 8 A 173 GLN PRO GLY THR LEU LEU GLY ARG TYR ALA ASN SER TYR SEQRES 9 A 173 ASN GLN ALA LEU CYS GLU GLY GLY GLN SER SER GLY PRO SEQRES 10 A 173 HIS VAL HIS PHE THR LEU LEU GLN ASN GLY GLN GLN VAL SEQRES 11 A 173 SER LEU HIS ASN ARG TYR ILE SER ASN TYR ARG ILE ASP SEQRES 12 A 173 VAL GLY ASN SER ASN TYR ASP SER ASN CYS ASN ASN PHE SEQRES 13 A 173 TYR PHE GLU ARG ASN GLY ARG ARG THR CYS ALA TRP ARG SEQRES 14 A 173 PRO LEU TYR ARG HET ZN A 201 1 HET GOL A 202 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *168(H2 O) HELIX 1 AA1 SER A 103 LEU A 108 1 6 SHEET 1 AA1 6 THR A 90 VAL A 91 0 SHEET 2 AA1 6 GLY A 55 SER A 61 -1 N GLY A 55 O VAL A 91 SHEET 3 AA1 6 ASN A 64 THR A 68 -1 O THR A 68 N VAL A 56 SHEET 4 AA1 6 PHE A 73 TYR A 78 -1 O TYR A 77 N ILE A 65 SHEET 5 AA1 6 VAL A 119 GLN A 125 -1 O LEU A 124 N ALA A 74 SHEET 6 AA1 6 GLN A 128 GLN A 129 -1 O GLN A 128 N GLN A 125 SHEET 1 AA2 8 THR A 90 VAL A 91 0 SHEET 2 AA2 8 GLY A 55 SER A 61 -1 N GLY A 55 O VAL A 91 SHEET 3 AA2 8 ASN A 64 THR A 68 -1 O THR A 68 N VAL A 56 SHEET 4 AA2 8 PHE A 73 TYR A 78 -1 O TYR A 77 N ILE A 65 SHEET 5 AA2 8 VAL A 119 GLN A 125 -1 O LEU A 124 N ALA A 74 SHEET 6 AA2 8 SER A 32 ASN A 36 -1 N LEU A 33 O PHE A 121 SHEET 7 AA2 8 TYR A 14 SER A 17 -1 N TYR A 16 O ASN A 36 SHEET 8 AA2 8 LEU A 171 TYR A 172 -1 O LEU A 171 N TRP A 15 SHEET 1 AA3 3 TRP A 48 GLN A 50 0 SHEET 2 AA3 3 LEU A 96 TYR A 100 -1 O GLY A 98 N VAL A 49 SHEET 3 AA3 3 MET A 80 SER A 81 -1 N SER A 81 O ARG A 99 SHEET 1 AA4 4 TYR A 136 ILE A 137 0 SHEET 2 AA4 4 TYR A 140 ASP A 143 -1 O TYR A 140 N ILE A 137 SHEET 3 AA4 4 TYR A 157 ARG A 160 -1 O GLU A 159 N ARG A 141 SHEET 4 AA4 4 ARG A 163 THR A 165 -1 O THR A 165 N PHE A 158 SSBOND 1 CYS A 63 CYS A 109 1555 1555 2.05 SSBOND 2 CYS A 153 CYS A 166 1555 1555 2.03 LINK NE2 HIS A 21 ZN ZN A 201 1555 1555 2.10 LINK OD1 ASP A 34 ZN ZN A 201 1555 1555 2.03 LINK ND1 HIS A 120 ZN ZN A 201 1555 1555 2.05 LINK ZN ZN A 201 O2 GOL A 202 1555 1555 2.21 CISPEP 1 TYR A 28 PRO A 29 0 -6.29 SITE 1 AC1 4 HIS A 21 ASP A 34 HIS A 120 GOL A 202 SITE 1 AC2 8 HIS A 21 ASP A 34 HIS A 79 GLN A 113 SITE 2 AC2 8 HIS A 118 HIS A 120 TYR A 149 ZN A 201 CRYST1 62.841 82.443 73.419 90.00 90.00 90.00 C 2 2 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 0.015913 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012130 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013620 0.00000