HEADER HYDROLASE 19-FEB-00 1C7K TITLE CRYSTAL STRUCTURE OF THE ZINC PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC ENDOPROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NCNP; COMPND 5 EC: 3.4.24.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES CAESPITOSUS; SOURCE 3 ORGANISM_TAXID: 53502 KEYWDS ALPHA AND BETA PROTEIN, METALLOPROTEINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.KURISU,S.HARADA,Y.KAI REVDAT 5 20-NOV-24 1C7K 1 REMARK REVDAT 4 27-DEC-23 1C7K 1 REMARK LINK REVDAT 3 04-OCT-17 1C7K 1 REMARK REVDAT 2 24-FEB-09 1C7K 1 VERSN REVDAT 1 25-APR-01 1C7K 0 JRNL AUTH G.KURISU,Y.KAI,S.HARADA JRNL TITL STRUCTURE OF THE ZINC-BINDING SITE IN THE CRYSTAL STRUCTURE JRNL TITL 2 OF A ZINC ENDOPROTEASE FROM STREPTOMYCES CAESPITOSUS AT 1 A JRNL TITL 3 RESOLUTION. JRNL REF J.INORG.BIOCHEM. V. 82 225 2000 JRNL REFN ISSN 0162-0134 JRNL PMID 11132632 JRNL DOI 10.1016/S0162-0134(00)00136-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.KURISU,T.KINOSHITA,A.SUGIMOTO,A.NAGARA,Y.KAI,N.KASAI, REMARK 1 AUTH 2 S.HARADA REMARK 1 TITL STRUCTURE OF THE ZINC ENDOPROTEASE FROM STREPTOMYCES REMARK 1 TITL 2 CAESPITOSUS REMARK 1 REF J.BIOCHEM.(TOKYO) V. 121 304 1997 REMARK 1 REFN ISSN 0021-924X REMARK 1 REFERENCE 2 REMARK 1 AUTH S.HARADA,T.KINOSHITA,N.KASAI,S.TSUNASAWA,F.SAKIYAMA REMARK 1 TITL COMPLETE AMINO ACID SEQUENCE OF A ZINC METALLOENDOPROTEASE REMARK 1 TITL 2 FROM STREPTOMYCES CAESPITOSUS REMARK 1 REF EUR.J.BIOCHEM. V. 233 683 1995 REMARK 1 REFN ISSN 0014-2956 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.HARADA,K.KITADOKORO,T.KINOSHITA,Y.KAI,N.KASAI REMARK 1 TITL CRYSTALLIZATION AND MAIN-CHAIN STRUCTURE OF NEUTRAL PROTEASE REMARK 1 TITL 2 FROM STREPTOMYCES CAESPITOSUS REMARK 1 REF J.BIOCHEM.(TOKYO) V. 110 46 1991 REMARK 1 REFN ISSN 0021-924X REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.154 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.148 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 344 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4713 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.147 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.131 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 341 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3372 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1015 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1133.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 992 REMARK 3 NUMBER OF RESTRAINTS : 1187 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.080 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.090 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.050 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C7K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000005003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7107 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59541 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.3 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONE, PH 7.0, LIQUID DIFFUSION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.55150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.62150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.59950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 18.62150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.55150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.59950 REMARK 290 SMTRY3 4 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 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR A 116 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 124 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES 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 CA A 134 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 76 OD1 REMARK 620 2 ASP A 76 OD2 50.8 REMARK 620 3 THR A 78 OG1 79.6 126.1 REMARK 620 4 HOH A 204 O 126.6 77.3 153.1 REMARK 620 5 HOH A 205 O 71.4 79.9 105.6 90.3 REMARK 620 6 HOH A 215 O 80.1 78.4 72.9 103.3 151.0 REMARK 620 7 HOH A 219 O 147.6 135.2 76.3 77.3 136.2 72.4 REMARK 620 8 HOH A 222 O 134.0 145.1 83.0 81.2 73.0 133.7 63.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 133 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 NE2 REMARK 620 2 HIS A 87 NE2 106.5 REMARK 620 3 ASP A 93 OD1 148.6 82.1 REMARK 620 4 ASP A 93 OD2 103.5 101.9 45.2 REMARK 620 5 HOH A 202 O 104.5 117.0 97.7 121.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZIN REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ZINC COORDINATION REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 134 DBREF 1C7K A 1 132 UNP P56406 SNPA_STRCS 1 132 SEQRES 1 A 132 THR VAL THR VAL THR TYR ASP PRO SER ASN ALA PRO SER SEQRES 2 A 132 PHE GLN GLN GLU ILE ALA ASN ALA ALA GLN ILE TRP ASN SEQRES 3 A 132 SER SER VAL ARG ASN VAL GLN LEU ARG ALA GLY GLY ASN SEQRES 4 A 132 ALA ASP PHE SER TYR TYR GLU GLY ASN ASP SER ARG GLY SEQRES 5 A 132 SER TYR ALA GLN THR ASP GLY HIS GLY ARG GLY TYR ILE SEQRES 6 A 132 PHE LEU ASP TYR GLN GLN ASN GLN GLN TYR ASP SER THR SEQRES 7 A 132 ARG VAL THR ALA HIS GLU THR GLY HIS VAL LEU GLY LEU SEQRES 8 A 132 PRO ASP HIS TYR GLN GLY PRO CYS SER GLU LEU MET SER SEQRES 9 A 132 GLY GLY GLY PRO GLY PRO SER CYS THR ASN PRO TYR PRO SEQRES 10 A 132 ASN ALA GLN GLU ARG SER ARG VAL ASN ALA LEU TRP ALA SEQRES 11 A 132 ASN GLY HET ZN A 133 1 HET CA A 134 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 CA CA 2+ FORMUL 4 HOH *116(H2 O) HELIX 1 1 ALA A 11 SER A 13 5 3 HELIX 2 2 PHE A 14 VAL A 29 1 16 HELIX 3 3 TYR A 69 TYR A 75 1 7 HELIX 4 4 ASP A 76 GLY A 90 1 15 HELIX 5 5 GLU A 101 GLY A 105 5 5 HELIX 6 6 ASN A 118 TRP A 129 1 12 SHEET 1 A 5 VAL A 32 ALA A 36 0 SHEET 2 A 5 VAL A 2 ASN A 10 1 O VAL A 2 N GLN A 33 SHEET 3 A 5 PHE A 42 GLY A 47 1 O PHE A 42 N ASP A 7 SHEET 4 A 5 GLY A 63 ASP A 68 1 O GLY A 63 N SER A 43 SHEET 5 A 5 TYR A 54 THR A 57 -1 O TYR A 54 N PHE A 66 SSBOND 1 CYS A 99 CYS A 112 1555 1555 2.04 LINK OD1 ASP A 76 CA CA A 134 1555 1555 2.59 LINK OD2 ASP A 76 CA CA A 134 1555 1555 2.49 LINK OG1 THR A 78 CA CA A 134 1555 1555 2.45 LINK NE2 HIS A 83 ZN ZN A 133 1555 1555 2.01 LINK NE2 HIS A 87 ZN ZN A 133 1555 1555 2.01 LINK OD1 ASP A 93 ZN ZN A 133 1555 1555 3.08 LINK OD2 ASP A 93 ZN ZN A 133 1555 1555 1.95 LINK ZN ZN A 133 O HOH A 202 1555 1555 1.93 LINK CA CA A 134 O HOH A 204 1555 4456 2.42 LINK CA CA A 134 O HOH A 205 1555 1555 2.42 LINK CA CA A 134 O HOH A 215 1555 1555 2.49 LINK CA CA A 134 O HOH A 219 1555 1555 2.51 LINK CA CA A 134 O HOH A 222 1555 1555 2.36 SITE 1 ZIN 4 HIS A 83 HIS A 87 ASP A 93 HOH A 202 SITE 1 AC1 4 HIS A 83 HIS A 87 ASP A 93 HOH A 202 SITE 1 AC2 7 ASP A 76 THR A 78 HOH A 204 HOH A 205 SITE 2 AC2 7 HOH A 215 HOH A 219 HOH A 222 CRYST1 55.103 55.199 37.243 90.00 90.00 90.00 P 21 21 21 4 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 0.018148 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026851 0.00000