HEADER HYDROLASE 24-SEP-10 2XS3 TITLE STRUCTURE OF KARILYSIN CATALYTIC MMP DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: KARILYSIN PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 35-200; COMPND 5 SYNONYM: KARILYSIN CATALYTIC DOMAIN KLY18; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PEPTIDE ALA-PHE-THR-SER; COMPND 9 CHAIN: C, D 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 2XS3 1 REMARK LINK REVDAT 3 15-MAY-19 2XS3 1 REMARK REVDAT 2 29-DEC-10 2XS3 1 JRNL REVDAT 1 03-NOV-10 2XS3 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 14703 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 708 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1001 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.4850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.20000 REMARK 3 B22 (A**2) : -1.70000 REMARK 3 B33 (A**2) : 1.99000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.422 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.203 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.868 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2795 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1803 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3807 ; 1.321 ; 1.919 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4380 ; 0.886 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 6.729 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;33.332 ;24.348 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 404 ;17.064 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;15.179 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 390 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3162 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 602 ; 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): 1682 ; 0.603 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 694 ; 0.106 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2688 ; 1.109 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1113 ; 1.460 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1119 ; 2.264 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 35 A 200 REMARK 3 RESIDUE RANGE : A 999 A 998 REMARK 3 ORIGIN FOR THE GROUP (A): -26.1290 18.0940 -8.3380 REMARK 3 T TENSOR REMARK 3 T11: 0.0523 T22: 0.0876 REMARK 3 T33: 0.1037 T12: 0.0147 REMARK 3 T13: -0.0103 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.9317 L22: 3.0221 REMARK 3 L33: 3.7876 L12: -0.2781 REMARK 3 L13: -1.0615 L23: 0.5305 REMARK 3 S TENSOR REMARK 3 S11: 0.0683 S12: 0.2506 S13: 0.0213 REMARK 3 S21: -0.3765 S22: -0.0667 S23: 0.1048 REMARK 3 S31: -0.2003 S32: -0.3439 S33: -0.0015 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 35 B 200 REMARK 3 RESIDUE RANGE : B 999 B 998 REMARK 3 ORIGIN FOR THE GROUP (A): 7.9390 18.3170 -25.9500 REMARK 3 T TENSOR REMARK 3 T11: 0.0723 T22: 0.1003 REMARK 3 T33: 0.0304 T12: 0.0087 REMARK 3 T13: -0.0001 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 3.5364 L22: 3.7925 REMARK 3 L33: 1.9424 L12: -0.1371 REMARK 3 L13: 0.7145 L23: -0.4956 REMARK 3 S TENSOR REMARK 3 S11: 0.1277 S12: 0.3158 S13: 0.0836 REMARK 3 S21: -0.1175 S22: -0.2118 S23: -0.3171 REMARK 3 S31: 0.0575 S32: 0.2463 S33: 0.0841 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 301 A 304 REMARK 3 RESIDUE RANGE : B 301 B 304 REMARK 3 RESIDUE RANGE : B 1305 B 1305 REMARK 3 ORIGIN FOR THE GROUP (A): -11.2940 17.0700 -18.2750 REMARK 3 T TENSOR REMARK 3 T11: 0.1807 T22: 0.2306 REMARK 3 T33: 0.0970 T12: -0.0024 REMARK 3 T13: -0.0462 T23: -0.0355 REMARK 3 L TENSOR REMARK 3 L11: 0.9331 L22: 0.7524 REMARK 3 L33: 0.7521 L12: -0.1869 REMARK 3 L13: -0.2519 L23: -0.2430 REMARK 3 S TENSOR REMARK 3 S11: 0.1208 S12: 0.2163 S13: -0.0417 REMARK 3 S21: -0.1622 S22: -0.1592 S23: 0.0622 REMARK 3 S31: -0.0727 S32: -0.0371 S33: 0.0384 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 2XS3 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_1290045504. 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15411 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 1MNC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION ASSAYS WERE PERFORMED REMARK 280 BY THE SITTING-DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTIONS REMARK 280 WERE PREPARED BY A TECAN ROBOT AND CRYSTALLIZATION DROPS WERE REMARK 280 DISPENSED ON 96X2-WELL MRC PLATES (INNOVADYNE) BY A CARTESIAN REMARK 280 (GENOMIC SOLUTIONS) NANODROP ROBOT AT THE HIGH-THROUGHPUT REMARK 280 CRYSTALLOGRAPHY PLATFORM AT BARCELONA SCIENCE PARK. CRYSTALS REMARK 280 SUITABLE FOR STRUCTURE ANALYSIS WERE OBTAINED FOR UNBOUND KLY18 REMARK 280 IN A BRUKER STEADY-TEMPERATURE CRYSTAL FARM AT 20C FROM DROPS REMARK 280 CONTAINING 100NL OF PROTEIN SOLUTION (AT 9MG ML-1 IN 5MM TRIS- REMARK 280 HCL, PH8.0, 0.02% SODIUM AZIDE) AND 100NL OF 45% 2-METHYL-2,4- REMARK 280 PENTANEDIOL, 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, PH8.5 AS REMARK 280 RESERVOIR SOLUTION., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 60.68500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.55500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.68500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.55500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 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: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.5 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 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 470 ASP B 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 HIS A 57 63.57 -170.44 REMARK 500 LEU A 58 133.70 -179.01 REMARK 500 THR A 112 24.01 85.02 REMARK 500 ASN A 143 -165.00 -77.33 REMARK 500 SER B 55 85.13 69.72 REMARK 500 THR B 112 -139.28 -120.35 REMARK 500 ARG B 182 48.31 -109.97 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 IONS OF EACH OF THE TWO PROTEIN MOLECULES A AND B. 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 998 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 102 NE2 REMARK 620 2 ASP A 104 OD2 108.7 REMARK 620 3 HIS A 117 NE2 119.1 114.9 REMARK 620 4 HIS A 133 ND1 112.4 92.7 105.8 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 101.9 REMARK 620 3 HIS A 165 NE2 117.7 93.7 REMARK 620 4 ALA C 201 O 80.7 174.1 89.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 998 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 102 NE2 REMARK 620 2 ASP B 104 OD2 103.6 REMARK 620 3 HIS B 117 NE2 114.0 109.5 REMARK 620 4 HIS B 133 ND1 107.9 105.5 115.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 155 NE2 REMARK 620 2 HIS B 159 NE2 100.8 REMARK 620 3 HIS B 165 NE2 111.5 90.9 REMARK 620 4 ALA D 201 O 89.8 168.6 89.2 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 ZN A 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B 1305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XS4 RELATED DB: PDB REMARK 900 STRUCTURE OF KARILYSIN CATALYTIC MMP DOMAIN IN COMPLEX WITH REMARK 900 MAGNESIUM REMARK 999 REMARK 999 SEQUENCE REMARK 999 ONLY THE CATALYTIC DOMAIN (TYR35-PHE200) 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-SER. AUTHOR SUGGESTS THAT REMARK 999 THIS PEPTIDE MAY HAVE BEEN RECRUITED BY THE ENZYME DURING REMARK 999 PROTEIN PRODUCTION/PURIFICATION/PROCESSING. DBREF 2XS3 A 35 200 UNP D0EM77 D0EM77_BACFO 35 200 DBREF 2XS3 B 35 200 UNP D0EM77 D0EM77_BACFO 35 200 DBREF 2XS3 C 201 204 PDB 2XS3 2XS3 201 204 DBREF 2XS3 D 201 204 PDB 2XS3 2XS3 201 204 SEQRES 1 A 166 TYR VAL LEU GLN GLY SER LYS TRP ASN LYS THR THR LEU SEQRES 2 A 166 LYS TYR TYR ILE TYR ASN SER SER SER HIS LEU THR THR SEQRES 3 A 166 THR GLU ARG GLU ASN ALA ILE ARG SER ALA PHE ALA LEU SEQRES 4 A 166 TRP SER ASP LYS SER THR LEU SER PHE ILE GLN VAL TYR SEQRES 5 A 166 ASN PRO ASN GLN ALA ASP ILE LYS ILE LYS TRP GLU LYS SEQRES 6 A 166 GLY ASN HIS GLY ASP GLY TYR PRO PHE ASP GLY ASN THR SEQRES 7 A 166 GLY ILE LEU ALA HIS ALA PHE TYR PRO PRO PRO ALA GLY SEQRES 8 A 166 GLY ASN TYR ALA GLY HIS LEU HIS PHE ASP ASP ASP GLU SEQRES 9 A 166 ASN TRP SER ILE ASN GLY SER GLY ILE ASP LEU ILE THR SEQRES 10 A 166 VAL ALA ALA HIS GLU ILE GLY HIS LEU LEU GLY ILE GLU SEQRES 11 A 166 HIS SER ASN VAL SER SER ALA LEU MET TYR PRO TYR TYR SEQRES 12 A 166 THR GLY ILE LYS ARG GLN LEU ASP ASN ASP ASP CYS LEU SEQRES 13 A 166 ALA VAL TRP ASP LEU TYR GLY TYR PRO PHE SEQRES 1 C 4 ALA PHE THR SER SEQRES 1 B 166 TYR VAL LEU GLN GLY SER LYS TRP ASN LYS THR THR LEU SEQRES 2 B 166 LYS TYR TYR ILE TYR ASN SER SER SER HIS LEU THR THR SEQRES 3 B 166 THR GLU ARG GLU ASN ALA ILE ARG SER ALA PHE ALA LEU SEQRES 4 B 166 TRP SER ASP LYS SER THR LEU SER PHE ILE GLN VAL TYR SEQRES 5 B 166 ASN PRO ASN GLN ALA ASP ILE LYS ILE LYS TRP GLU LYS SEQRES 6 B 166 GLY ASN HIS GLY ASP GLY TYR PRO PHE ASP GLY ASN THR SEQRES 7 B 166 GLY ILE LEU ALA HIS ALA PHE TYR PRO PRO PRO ALA GLY SEQRES 8 B 166 GLY ASN TYR ALA GLY HIS LEU HIS PHE ASP ASP ASP GLU SEQRES 9 B 166 ASN TRP SER ILE ASN GLY SER GLY ILE ASP LEU ILE THR SEQRES 10 B 166 VAL ALA ALA HIS GLU ILE GLY HIS LEU LEU GLY ILE GLU SEQRES 11 B 166 HIS SER ASN VAL SER SER ALA LEU MET TYR PRO TYR TYR SEQRES 12 B 166 THR GLY ILE LYS ARG GLN LEU ASP ASN ASP ASP CYS LEU SEQRES 13 B 166 ALA VAL TRP ASP LEU TYR GLY TYR PRO PHE SEQRES 1 D 4 ALA PHE THR SER HET ZN A 998 1 HET ZN A 999 1 HET ZN B 998 1 HET ZN B 999 1 HET TRS B1305 8 HETNAM ZN ZINC ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 5 ZN 4(ZN 2+) FORMUL 9 TRS C4 H12 N O3 1+ FORMUL 10 HOH *115(H2 O) HELIX 1 1 THR A 59 ASP A 76 1 18 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 HELIX 6 6 THR B 59 ASP B 76 1 18 HELIX 7 7 ASN B 87 ALA B 91 5 5 HELIX 8 8 GLY B 125 ALA B 129 5 5 HELIX 9 9 LEU B 149 GLY B 162 1 14 HELIX 10 10 ASP B 185 GLY B 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 SHEET 1 BA 5 SER B 81 GLN B 84 0 SHEET 2 BA 5 THR B 46 ILE B 51 1 O LEU B 47 N ILE B 83 SHEET 3 BA 5 ILE B 93 GLU B 98 1 O ILE B 93 N TYR B 50 SHEET 4 BA 5 HIS B 131 ASP B 135 1 O LEU B 132 N LYS B 96 SHEET 5 BA 5 ALA B 116 ALA B 118 -1 O HIS B 117 N HIS B 133 SHEET 1 BB 2 TRP B 140 SER B 141 0 SHEET 2 BB 2 ILE B 147 ASP B 148 1 O ILE B 147 N SER B 141 LINK NE2 HIS A 102 ZN ZN A 998 1555 1555 1.96 LINK OD2 ASP A 104 ZN ZN A 998 1555 1555 1.85 LINK NE2 HIS A 117 ZN ZN A 998 1555 1555 1.92 LINK ND1 HIS A 133 ZN ZN A 998 1555 1555 2.24 LINK NE2 HIS A 155 ZN ZN A 999 1555 1555 1.91 LINK NE2 HIS A 159 ZN ZN A 999 1555 1555 2.20 LINK NE2 HIS A 165 ZN ZN A 999 1555 1555 2.04 LINK ZN ZN A 999 O ALA C 201 1555 1555 2.34 LINK NE2 HIS B 102 ZN ZN B 998 1555 1555 2.21 LINK OD2 ASP B 104 ZN ZN B 998 1555 1555 1.98 LINK NE2 HIS B 117 ZN ZN B 998 1555 1555 2.04 LINK ND1 HIS B 133 ZN ZN B 998 1555 1555 2.19 LINK NE2 HIS B 155 ZN ZN B 999 1555 1555 2.06 LINK NE2 HIS B 159 ZN ZN B 999 1555 1555 2.26 LINK NE2 HIS B 165 ZN ZN B 999 1555 1555 2.02 LINK ZN ZN B 999 O ALA D 201 1555 1555 2.32 CISPEP 1 PRO A 122 PRO A 123 0 -4.53 CISPEP 2 PRO B 122 PRO B 123 0 -3.55 SITE 1 AC1 4 HIS A 102 ASP A 104 HIS A 117 HIS A 133 SITE 1 AC2 4 HIS A 155 HIS A 159 HIS A 165 ALA C 201 SITE 1 AC3 4 HIS B 102 ASP B 104 HIS B 117 HIS B 133 SITE 1 AC4 4 HIS B 155 HIS B 159 HIS B 165 ALA D 201 SITE 1 AC5 4 TYR B 106 ALA B 118 PHE B 119 GLN B 183 CRYST1 121.370 53.110 86.300 90.00 134.55 90.00 C 1 2 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 0.008239 0.000000 0.008111 0.00000 SCALE2 0.000000 0.018829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016260 0.00000