HEADER HYDROLASE 24-SEP-10 2XS4 TITLE STRUCTURE OF KARILYSIN CATALYTIC MMP DOMAIN IN COMPLEX WITH MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: KARILYSIN PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 35-201; COMPND 5 SYNONYM: KARILYSIN CATALYTIC DOMAIN KLY18; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PEPTIDE ALA-PHE-THR; COMPND 9 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TANNERELLA FORSYTHIA; SOURCE 3 ORGANISM_TAXID: 28112; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, BACTERIAL MMP, VIRULENCE FACTOR, METALLOPROTEASE, ZINC- KEYWDS 2 DEPENDENT, PEPTIDASE EXPDTA X-RAY DIFFRACTION AUTHOR N.CERDA-COSTA,T.GUEVARA,A.Y.KARIM,M.KSIAZEK,K.-A.NGUYEN,J.L.AROLAS, AUTHOR 2 J.POTEMPA,F.X.GOMIS-RUTH REVDAT 4 20-DEC-23 2XS4 1 REMARK LINK REVDAT 3 15-MAY-19 2XS4 1 REMARK REVDAT 2 29-DEC-10 2XS4 1 JRNL REVDAT 1 03-NOV-10 2XS4 0 JRNL AUTH N.CERDA-COSTA,T.GUEVARA,A.Y.KARIM,M.KSIAZEK,K.A.NGUYEN, JRNL AUTH 2 J.L.AROLAS,J.POTEMPA,F.X.GOMIS-RUTH JRNL TITL THE STRUCTURE OF THE CATALYTIC DOMAIN OF TANNERELLA JRNL TITL 2 FORSYTHIA KARILYSIN REVEALS IT IS A BACTERIAL XENOLOGUE OF JRNL TITL 3 ANIMAL MATRIX METALLOPROTEINASES. JRNL REF MOL.MICROBIOL. V. 79 119 2011 JRNL REFN ISSN 0950-382X JRNL PMID 21166898 JRNL DOI 10.1111/J.1365-2958.2010.07434.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.Y.KARIM,M.KULCZYCKA,T.KANTYKA,G.DUBIN,A.JABAIAH, REMARK 1 AUTH 2 P.S.DAUGHERTY,I.B.THOGERSEN,J.J.ENGHILD,K.NGUYEN,J.POTEMPA REMARK 1 TITL A NOVEL MATRIX METALLOPROTEASE-LIKE ENZYME (KARILYSIN) OF REMARK 1 TITL 2 THE PERIODONTAL PATHOGEN TANNERELLA FORSYTHIA ATCC 43037. REMARK 1 REF BIOL.CHEM. V. 391 105 2010 REMARK 1 REFN ISSN 1431-6730 REMARK 1 PMID 19919176 REMARK 1 DOI 10.1515/BC.2010.009 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.KOZIEL,A.Y.KARIM,K.PRZYBYSZEWSKA,M.KSIAZEK,M.RAPALA-KOZIK, REMARK 1 AUTH 2 K.NGUYEN,J.POTEMPA REMARK 1 TITL PROTEOLYTIC INACTIVATION OF LL-37 BY KARILYSIN, A NOVEL REMARK 1 TITL 2 VIRULENCE MECHANISM OF TANNERELLA FORSYTHIA. REMARK 1 REF J.INNATE.IMMUN. V. 2 288 2010 REMARK 1 REFN ISSN 1662-811X REMARK 1 PMID 20375548 REMARK 1 DOI 10.1159/000281881 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 20403 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.900 REMARK 3 FREE R VALUE TEST SET COUNT : 820 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1399 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1351 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 196 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -0.37000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.508 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1394 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 898 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1899 ; 1.034 ; 1.916 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2182 ; 0.822 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 168 ; 5.292 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;35.114 ;24.348 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 202 ;11.698 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;16.538 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 195 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1581 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 301 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 839 ; 0.464 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 347 ; 0.084 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1341 ; 0.873 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 555 ; 1.225 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 558 ; 1.959 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 35 A 201 REMARK 3 RESIDUE RANGE : A 999 A 999 REMARK 3 RESIDUE RANGE : A 998 A 998 REMARK 3 RESIDUE RANGE : A 997 A 997 REMARK 3 ORIGIN FOR THE GROUP (A): 23.7456 12.6837 18.3271 REMARK 3 T TENSOR REMARK 3 T11: 0.0265 T22: 0.0372 REMARK 3 T33: 0.0276 T12: -0.0094 REMARK 3 T13: -0.0116 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.4081 L22: 1.9225 REMARK 3 L33: 1.5838 L12: -0.4259 REMARK 3 L13: 0.1384 L23: 0.2696 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: -0.0035 S13: 0.0237 REMARK 3 S21: 0.0307 S22: 0.0539 S23: -0.2170 REMARK 3 S31: 0.0304 S32: 0.2064 S33: -0.0418 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 301 B 303 REMARK 3 RESIDUE RANGE : A 1202 A 1202 REMARK 3 RESIDUE RANGE : A 2001 A 2196 REMARK 3 ORIGIN FOR THE GROUP (A): 21.7176 14.5926 19.1491 REMARK 3 T TENSOR REMARK 3 T11: 0.1368 T22: 0.1399 REMARK 3 T33: 0.1228 T12: -0.0264 REMARK 3 T13: 0.0103 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 1.8784 L22: 1.4070 REMARK 3 L33: 1.4383 L12: -0.6342 REMARK 3 L13: 0.4491 L23: -0.0489 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: 0.0488 S13: 0.0475 REMARK 3 S21: 0.0342 S22: 0.0412 S23: -0.1238 REMARK 3 S31: 0.0682 S32: 0.0642 S33: -0.0179 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2XS4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1290045509. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21225 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.80 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 2XS3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF MAGNESIUM-BOUND KLY18 WERE REMARK 280 OBTAINED AT 4C BY MIXING PROTEIN SOLUTION PREINCUBATED WITH REMARK 280 CALCIUM (AT 7.3MG ML-1 IN 5MM TRIS-HCL, PH8.0, 5MM CALCIUM REMARK 280 CHLORIDE, 0.02% SODIUM AZIDE) AND 14% SODIUM POLYACRYLATE 5100, REMARK 280 20MM MAGNESIUM CHLORIDE, 0.1M HEPES, PH7.5 IN A VOLUME RATIO OF REMARK 280 1:3. THE LATTER CONDITIONS WERE SCALED UP TO THE MICROLITER REMARK 280 RANGE WITH 24-WELL CRYSCHEM CRYSTALLIZATION DISHES (HAMPTON REMARK 280 RESEARCH)., TEMPERATURE 277K 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 42.89500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.89500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.74000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.89500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.89500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.74000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 42.89500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 42.89500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 26.74000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 42.89500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 42.89500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.74000 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: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 ASP A 136 CB CG OD1 OD2 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 ASP A 109 58.76 75.64 REMARK 500 ASN A 111 -38.40 -158.28 REMARK 500 LEU A 115 -72.55 70.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ZINC CATION (ZN): CATALYTIC 999 AND STRUCTURAL 998 ZINC REMARK 600 CATIONS. REMARK 600 MAGNESIUM CATION (MG): TENTATIVELY TRACED BASED ON LIGAND REMARK 600 GEOMETRY AND ELECTRON DENSITY CONSIDERATIONS. 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 A 997 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 75 O REMARK 620 2 SER A 78 O 85.8 REMARK 620 3 HOH A2070 O 100.8 92.9 REMARK 620 4 HOH A2072 O 86.8 83.9 171.6 REMARK 620 5 HOH A2192 O 87.7 172.2 84.1 100.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 998 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 102 NE2 REMARK 620 2 ASP A 104 OD1 107.5 REMARK 620 3 HIS A 117 NE2 118.1 118.1 REMARK 620 4 HIS A 133 ND1 103.6 92.4 113.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 155 NE2 REMARK 620 2 HIS A 159 NE2 94.4 REMARK 620 3 HIS A 165 NE2 112.9 96.4 REMARK 620 4 ALA B 301 O 92.1 171.4 86.2 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 MG A 997 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XS3 RELATED DB: PDB REMARK 900 STRUCTURE OF KARILYSIN CATALYTIC MMP DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 ONLY THE CATALYTIC DOMAIN (TYR35-SER201) WAS CRYSTALLIZED. REMARK 999 A PEPTIDE WAS FOUND AT THE ACTIVE SITE OF THE PROTEIN, WHICH REMARK 999 HAS BEEN INTERPRETED AS ALA-PHE-THR. AUTHOR SUGGESTS THAT REMARK 999 THIS PEPTIDE MAY HAVE BEEN RECRUITED BY THE ENZYME DURING REMARK 999 PROTEIN PRODUCTION/PURIFICATION/PROCESSING. DBREF 2XS4 A 35 201 UNP D0EM77 D0EM77_BACFO 35 201 DBREF 2XS4 B 301 303 PDB 2XS4 2XS4 301 303 SEQRES 1 A 167 TYR VAL LEU GLN GLY SER LYS TRP ASN LYS THR THR LEU SEQRES 2 A 167 LYS TYR TYR ILE TYR ASN SER SER SER HIS LEU THR THR SEQRES 3 A 167 THR GLU ARG GLU ASN ALA ILE ARG SER ALA PHE ALA LEU SEQRES 4 A 167 TRP SER ASP LYS SER THR LEU SER PHE ILE GLN VAL TYR SEQRES 5 A 167 ASN PRO ASN GLN ALA ASP ILE LYS ILE LYS TRP GLU LYS SEQRES 6 A 167 GLY ASN HIS GLY ASP GLY TYR PRO PHE ASP GLY ASN THR SEQRES 7 A 167 GLY ILE LEU ALA HIS ALA PHE TYR PRO PRO PRO ALA GLY SEQRES 8 A 167 GLY ASN TYR ALA GLY HIS LEU HIS PHE ASP ASP ASP GLU SEQRES 9 A 167 ASN TRP SER ILE ASN GLY SER GLY ILE ASP LEU ILE THR SEQRES 10 A 167 VAL ALA ALA HIS GLU ILE GLY HIS LEU LEU GLY ILE GLU SEQRES 11 A 167 HIS SER ASN VAL SER SER ALA LEU MET TYR PRO TYR TYR SEQRES 12 A 167 THR GLY ILE LYS ARG GLN LEU ASP ASN ASP ASP CYS LEU SEQRES 13 A 167 ALA VAL TRP ASP LEU TYR GLY TYR PRO PHE SER SEQRES 1 B 3 ALA PHE THR HET MG A 997 1 HET ZN A 998 1 HET ZN A 999 1 HET CL A1202 1 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 3 MG MG 2+ FORMUL 4 ZN 2(ZN 2+) FORMUL 6 CL CL 1- FORMUL 7 HOH *196(H2 O) HELIX 1 1 THR A 59 LYS A 77 1 19 HELIX 2 2 ASN A 87 ALA A 91 5 5 HELIX 3 3 GLY A 125 ALA A 129 5 5 HELIX 4 4 LEU A 149 GLY A 162 1 14 HELIX 5 5 ASP A 185 GLY A 197 1 13 SHEET 1 AA 5 SER A 81 GLN A 84 0 SHEET 2 AA 5 THR A 46 ILE A 51 1 O LEU A 47 N ILE A 83 SHEET 3 AA 5 ILE A 93 GLU A 98 1 O ILE A 93 N TYR A 50 SHEET 4 AA 5 HIS A 131 ASP A 135 1 O LEU A 132 N LYS A 96 SHEET 5 AA 5 ALA A 116 ALA A 118 -1 O HIS A 117 N HIS A 133 SHEET 1 AB 2 TRP A 140 SER A 141 0 SHEET 2 AB 2 ILE A 147 ASP A 148 1 O ILE A 147 N SER A 141 LINK O SER A 75 MG MG A 997 1555 1555 2.32 LINK O SER A 78 MG MG A 997 1555 1555 2.28 LINK NE2 HIS A 102 ZN ZN A 998 1555 1555 2.01 LINK OD1 ASP A 104 ZN ZN A 998 1555 1555 2.04 LINK NE2 HIS A 117 ZN ZN A 998 1555 1555 1.99 LINK ND1 HIS A 133 ZN ZN A 998 1555 1555 2.07 LINK NE2 HIS A 155 ZN ZN A 999 1555 1555 2.03 LINK NE2 HIS A 159 ZN ZN A 999 1555 1555 2.16 LINK NE2 HIS A 165 ZN ZN A 999 1555 1555 2.07 LINK MG MG A 997 O HOH A2070 1555 1555 2.20 LINK MG MG A 997 O HOH A2072 1555 1555 2.06 LINK MG MG A 997 O HOH A2192 1555 4555 2.49 LINK ZN ZN A 999 O ALA B 301 1555 1555 2.24 CISPEP 1 ASN A 111 THR A 112 0 0.99 CISPEP 2 PRO A 122 PRO A 123 0 3.30 SITE 1 AC1 5 SER A 75 SER A 78 HOH A2070 HOH A2072 SITE 2 AC1 5 HOH A2192 SITE 1 AC2 4 HIS A 102 ASP A 104 HIS A 117 HIS A 133 SITE 1 AC3 4 HIS A 155 HIS A 159 HIS A 165 ALA B 301 SITE 1 AC4 5 ASN A 87 ASN A 143 GLY A 144 SER A 145 SITE 2 AC4 5 HOH A2132 CRYST1 85.790 85.790 53.480 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 0.011656 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018699 0.00000