HEADER HYDROLASE 27-FEB-12 4DWW TITLE CRYSTAL STRUCTURE OF NATTOKINASE FROM BACILLUS SUBTILIS NATTO COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUBTILISIN NAT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NATTOKINASE; COMPND 5 EC: 3.4.21.62 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. NATTO; SOURCE 3 ORGANISM_TAXID: 86029 KEYWDS FIBRINOLYTIC ACTIVITY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.CHATAKE,Y.YANAGISAWA REVDAT 2 08-NOV-23 4DWW 1 REMARK LINK REVDAT 1 14-MAR-12 4DWW 0 JRNL AUTH Y.YANAGISAWA,T.CHATAKE,K.CHIBA-KAMOSHIDA,S.NAITO,T.OHSUGI, JRNL AUTH 2 H.SUMI,I.YASUDA,Y.MORIMOTO JRNL TITL PURIFICATION, CRYSTALLIZATION AND PRELIMINARY X-RAY JRNL TITL 2 DIFFRACTION EXPERIMENT OF NATTOKINASE FROM BACILLUS SUBTILIS JRNL TITL 3 NATTO JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 66 1670 2010 JRNL REFN ESSN 1744-3091 JRNL PMID 21139221 JRNL DOI 10.1107/S1744309110043137 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 69.5 REMARK 3 NUMBER OF REFLECTIONS : 14732 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 760 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 41.3806 - 2.9754 0.71 2916 160 0.1360 0.1912 REMARK 3 2 2.9754 - 2.3617 0.81 3278 164 0.1337 0.1744 REMARK 3 3 2.3617 - 2.0632 0.80 3217 176 0.1253 0.2054 REMARK 3 4 2.0632 - 1.8745 0.71 2803 174 0.1317 0.2307 REMARK 3 5 1.8745 - 1.7402 0.44 1758 86 0.1433 0.2357 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 39.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.68030 REMARK 3 B22 (A**2) : -3.25770 REMARK 3 B33 (A**2) : 5.93800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.66110 REMARK 3 B23 (A**2) : 0.00000 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 2003 REMARK 3 ANGLE : 0.974 2739 REMARK 3 CHIRALITY : 0.063 318 REMARK 3 PLANARITY : 0.005 357 REMARK 3 DIHEDRAL : 12.796 691 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 4DWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070884. 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 : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6500 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14847 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 69.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1SCJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6.4MG/ML NATTOKINASE, 50MM TRIS HCL, REMARK 280 50MM HEPES, 10% PEG 8000, 8% ETHYLENE GLYCOL, 5MM CACL2, 100MM REMARK 280 NACL, 2MM PMSF, 4MM PEFABLOC SC, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 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 37.14650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.94950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.14650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.94950 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 537 LIES ON A SPECIAL POSITION. 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 ASN A 25 -4.07 76.41 REMARK 500 ASP A 32 -149.51 -165.34 REMARK 500 SER A 63 -23.74 97.89 REMARK 500 ALA A 73 32.13 -153.02 REMARK 500 ASN A 77 -157.93 -163.39 REMARK 500 VAL A 81 -166.06 -119.58 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 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 2 OE1 REMARK 620 2 ASP A 41 OD1 152.6 REMARK 620 3 ASP A 41 OD2 154.4 52.2 REMARK 620 4 LEU A 75 O 77.8 86.6 107.1 REMARK 620 5 ASN A 77 OD1 81.8 77.0 122.1 94.0 REMARK 620 6 ILE A 79 O 92.0 98.9 86.2 166.0 74.9 REMARK 620 7 VAL A 81 O 79.3 123.0 75.8 88.2 160.0 99.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 169 O REMARK 620 2 TYR A 171 O 94.6 REMARK 620 3 THR A 174 O 155.9 96.2 REMARK 620 4 THR A 174 OG1 85.4 74.3 76.9 REMARK 620 5 HOH A 416 O 104.9 110.9 91.3 167.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 302 DBREF 4DWW A 1 275 UNP P35835 SUBN_BACNA 107 381 SEQRES 1 A 275 ALA GLN SER VAL PRO TYR GLY ILE SER GLN ILE LYS ALA SEQRES 2 A 275 PRO ALA LEU HIS SER GLN GLY TYR THR GLY SER ASN VAL SEQRES 3 A 275 LYS VAL ALA VAL ILE ASP SER GLY ILE ASP SER SER HIS SEQRES 4 A 275 PRO ASP LEU ASN VAL ARG GLY GLY ALA SER PHE VAL PRO SEQRES 5 A 275 SER GLU THR ASN PRO TYR GLN ASP GLY SER SER HIS GLY SEQRES 6 A 275 THR HIS VAL ALA GLY THR ILE ALA ALA LEU ASN ASN SER SEQRES 7 A 275 ILE GLY VAL LEU GLY VAL ALA PRO SER ALA SER LEU TYR SEQRES 8 A 275 ALA VAL LYS VAL LEU ASP SER THR GLY SER GLY GLN TYR SEQRES 9 A 275 SER TRP ILE ILE ASN GLY ILE GLU TRP ALA ILE SER ASN SEQRES 10 A 275 ASN MET ASP VAL ILE ASN MET SER LEU GLY GLY PRO THR SEQRES 11 A 275 GLY SER THR ALA LEU LYS THR VAL VAL ASP LYS ALA VAL SEQRES 12 A 275 SER SER GLY ILE VAL VAL ALA ALA ALA ALA GLY ASN GLU SEQRES 13 A 275 GLY SER SER GLY SER THR SER THR VAL GLY TYR PRO ALA SEQRES 14 A 275 LYS TYR PRO SER THR ILE ALA VAL GLY ALA VAL ASN SER SEQRES 15 A 275 SER ASN GLN ARG ALA SER PHE SER SER VAL GLY SER GLU SEQRES 16 A 275 LEU ASP VAL MET ALA PRO GLY VAL SER ILE GLN SER THR SEQRES 17 A 275 LEU PRO GLY GLY THR TYR GLY ALA TYR ASN GLY THR SEB SEQRES 18 A 275 MET ALA THR PRO HIS VAL ALA GLY ALA ALA ALA LEU ILE SEQRES 19 A 275 LEU SER LYS HIS PRO THR TRP THR ASN ALA GLN VAL ARG SEQRES 20 A 275 ASP ARG LEU GLU SER THR ALA THR TYR LEU GLY ASN SER SEQRES 21 A 275 PHE TYR TYR GLY LYS GLY LEU ILE ASN VAL GLN ALA ALA SEQRES 22 A 275 ALA GLN MODRES 4DWW SEB A 221 SER O-BENZYLSULFONYL-SERINE HET SEB A 221 16 HET CA A 301 1 HET CA A 302 1 HETNAM SEB O-BENZYLSULFONYL-SERINE HETNAM CA CALCIUM ION FORMUL 1 SEB C10 H13 N O5 S FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *341(H2 O) HELIX 1 1 PRO A 5 ILE A 11 1 7 HELIX 2 2 LYS A 12 GLN A 19 1 8 HELIX 3 3 SER A 63 ALA A 74 1 12 HELIX 4 4 GLN A 103 ASN A 117 1 15 HELIX 5 5 SER A 132 SER A 145 1 14 HELIX 6 6 GLY A 219 HIS A 238 1 20 HELIX 7 7 THR A 242 THR A 253 1 12 HELIX 8 8 ASN A 259 GLY A 264 1 6 HELIX 9 9 ASN A 269 ALA A 274 1 6 SHEET 1 A 7 VAL A 44 SER A 49 0 SHEET 2 A 7 SER A 89 LYS A 94 1 O LEU A 90 N ARG A 45 SHEET 3 A 7 LYS A 27 ASP A 32 1 N VAL A 28 O SER A 89 SHEET 4 A 7 VAL A 121 MET A 124 1 O VAL A 121 N ALA A 29 SHEET 5 A 7 VAL A 148 ALA A 152 1 O VAL A 148 N ILE A 122 SHEET 6 A 7 ILE A 175 VAL A 180 1 O ILE A 175 N VAL A 149 SHEET 7 A 7 VAL A 198 PRO A 201 1 O VAL A 198 N GLY A 178 SHEET 1 B 2 ILE A 205 LEU A 209 0 SHEET 2 B 2 THR A 213 TYR A 217 -1 O THR A 213 N LEU A 209 LINK C THR A 220 N SEB A 221 1555 1555 1.33 LINK C SEB A 221 N MET A 222 1555 1555 1.33 LINK OE1 GLN A 2 CA CA A 302 1555 1555 2.49 LINK OD1 ASP A 41 CA CA A 302 1555 1555 2.43 LINK OD2 ASP A 41 CA CA A 302 1555 1555 2.62 LINK O LEU A 75 CA CA A 302 1555 1555 2.43 LINK OD1 ASN A 77 CA CA A 302 1555 1555 2.51 LINK O ILE A 79 CA CA A 302 1555 1555 2.43 LINK O VAL A 81 CA CA A 302 1555 1555 2.43 LINK O ALA A 169 CA CA A 301 1555 1555 2.31 LINK O TYR A 171 CA CA A 301 1555 1555 2.50 LINK O THR A 174 CA CA A 301 1555 1555 2.42 LINK OG1 THR A 174 CA CA A 301 1555 1555 2.58 LINK CA CA A 301 O HOH A 416 1555 1555 2.60 CISPEP 1 TYR A 167 PRO A 168 0 5.49 SITE 1 AC1 5 ALA A 169 TYR A 171 THR A 174 ASP A 197 SITE 2 AC1 5 HOH A 416 SITE 1 AC2 6 GLN A 2 ASP A 41 LEU A 75 ASN A 77 SITE 2 AC2 6 ILE A 79 VAL A 81 CRYST1 74.293 49.899 56.338 90.00 95.24 90.00 C 1 2 1 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 0.013460 0.000000 0.001234 0.00000 SCALE2 0.000000 0.020040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017824 0.00000