HEADER HYDROLASE 09-DEC-02 1NDQ TITLE BACILLUS LENTUS SUBTILISIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUBTILISIN SAVINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKALINE PROTEASE; COMPND 5 EC: 3.4.21.62 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LENTUS; SOURCE 3 ORGANISM_TAXID: 1467 KEYWDS SUBTILISIN, PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.PAN,R.BOTT,C.E.GLATZ REVDAT 5 14-FEB-24 1NDQ 1 REMARK LINK REVDAT 4 11-OCT-17 1NDQ 1 REMARK REVDAT 3 24-FEB-09 1NDQ 1 VERSN REVDAT 2 01-MAR-05 1NDQ 1 JRNL REVDAT 1 06-APR-04 1NDQ 0 JRNL AUTH X.PAN,R.BOTT,C.E.GLATZ JRNL TITL SUBTILISIN SURFACE PROPERTIES AND CRYSTAL GROWTH KINETICS JRNL REF J.CRYST.GROWTH V. 254 492 2003 JRNL REFN ISSN 0022-0248 JRNL DOI 10.1016/S0022-0248(03)01178-3 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.174 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.174 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 915 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18308 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1880 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : SHELXL97 REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000017787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 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: CNX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 23.80000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.90000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.90000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.80000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.20000 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 145 NE - CZ - NH1 ANGL. DEV. = -5.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 32 -150.16 -160.96 REMARK 500 ALA A 73 28.73 -145.52 REMARK 500 ASN A 77 -152.19 -161.36 REMARK 500 VAL A 81 -164.21 -120.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 41 0.07 SIDE CHAIN 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 276 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 2 OE1 REMARK 620 2 ASP A 41 OD1 153.6 REMARK 620 3 ASP A 41 OD2 151.8 53.8 REMARK 620 4 LEU A 75 O 77.5 87.6 107.4 REMARK 620 5 ASN A 77 OD1 79.3 77.9 128.2 85.6 REMARK 620 6 ILE A 79 O 86.3 101.5 93.7 158.3 77.3 REMARK 620 7 VAL A 81 O 76.7 125.9 75.4 91.3 155.9 98.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 277 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 169 O REMARK 620 2 TYR A 171 O 95.7 REMARK 620 3 ALA A 174 O 109.7 90.8 REMARK 620 4 HOH A 332 O 131.7 129.3 88.8 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 CA A 276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 277 DBREF 1NDQ A 1 275 UNP P29600 SUBS_BACLE 1 269 SEQRES 1 A 269 ALA GLN SER VAL PRO TRP GLY ILE SER ARG VAL GLN ALA SEQRES 2 A 269 PRO ALA ALA HIS ASN ARG GLY LEU THR GLY SER GLY VAL SEQRES 3 A 269 LYS VAL ALA VAL LEU ASP THR GLY ILE SER THR HIS PRO SEQRES 4 A 269 ASP LEU ASN ILE ARG GLY GLY ALA SER PHE VAL PRO GLY SEQRES 5 A 269 GLU PRO SER THR GLN ASP GLY ASN GLY HIS GLY THR HIS SEQRES 6 A 269 VAL ALA GLY THR ILE ALA ALA LEU ASN ASN SER ILE GLY SEQRES 7 A 269 VAL LEU GLY VAL ALA PRO SER ALA GLU LEU TYR ALA VAL SEQRES 8 A 269 LYS VAL LEU GLY ALA SER GLY SER GLY SER VAL SER SER SEQRES 9 A 269 ILE ALA GLN GLY LEU GLU TRP ALA GLY ASN ASN GLY MET SEQRES 10 A 269 HIS VAL ALA ASN LEU SER LEU GLY SER PRO SER PRO SER SEQRES 11 A 269 ALA THR LEU GLU GLN ALA VAL ASN SER ALA THR SER ARG SEQRES 12 A 269 GLY VAL LEU VAL VAL ALA ALA SER GLY ASN SER GLY ALA SEQRES 13 A 269 GLY SER ILE SER TYR PRO ALA ARG TYR ALA ASN ALA MET SEQRES 14 A 269 ALA VAL GLY ALA THR ASP GLN ASN ASN ASN ARG ALA SER SEQRES 15 A 269 PHE SER GLN TYR GLY ALA GLY LEU ASP ILE VAL ALA PRO SEQRES 16 A 269 GLY VAL ASN VAL GLN SER THR TYR PRO GLY SER THR TYR SEQRES 17 A 269 ALA SER LEU ASN GLY THR SER MET ALA THR PRO HIS VAL SEQRES 18 A 269 ALA GLY ALA ALA ALA LEU VAL LYS GLN LYS ASN PRO SER SEQRES 19 A 269 TRP SER ASN VAL GLN ILE ARG ASN HIS LEU LYS ASN THR SEQRES 20 A 269 ALA THR SER LEU GLY SER THR ASN LEU TYR GLY SER GLY SEQRES 21 A 269 LEU VAL ASN ALA GLU ALA ALA THR ARG HET CA A 276 1 HET CA A 277 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *84(H2 O) HELIX 1 1 PRO A 5 VAL A 11 1 7 HELIX 2 2 GLN A 12 ARG A 19 1 8 HELIX 3 3 GLY A 63 ALA A 74 1 12 HELIX 4 4 SER A 103 ASN A 117 1 15 HELIX 5 5 SER A 132 GLY A 146 1 15 HELIX 6 6 GLY A 219 ASN A 238 1 20 HELIX 7 7 SER A 242 THR A 253 1 12 HELIX 8 8 SER A 259 GLY A 264 1 6 HELIX 9 9 ASN A 269 THR A 274 1 6 SHEET 1 A 7 ILE A 44 SER A 49 0 SHEET 2 A 7 GLU A 89 LYS A 94 1 O ALA A 92 N GLY A 46 SHEET 3 A 7 LYS A 27 ASP A 32 1 N VAL A 28 O GLU A 89 SHEET 4 A 7 VAL A 121 LEU A 124 1 O ASN A 123 N ALA A 29 SHEET 5 A 7 LEU A 148 ALA A 152 1 O VAL A 150 N LEU A 124 SHEET 6 A 7 MET A 175 THR A 180 1 O VAL A 177 N ALA A 151 SHEET 7 A 7 LEU A 196 PRO A 201 1 O ILE A 198 N GLY A 178 SHEET 1 B 2 VAL A 205 TYR A 209 0 SHEET 2 B 2 THR A 213 LEU A 217 -1 O THR A 213 N TYR A 209 LINK OE1 GLN A 2 CA CA A 276 1555 1555 2.46 LINK OD1 ASP A 41 CA CA A 276 1555 1555 2.29 LINK OD2 ASP A 41 CA CA A 276 1555 1555 2.46 LINK O LEU A 75 CA CA A 276 1555 1555 2.32 LINK OD1 ASN A 77 CA CA A 276 1555 1555 2.46 LINK O ILE A 79 CA CA A 276 1555 1555 2.34 LINK O VAL A 81 CA CA A 276 1555 1555 2.39 LINK O ALA A 169 CA CA A 277 1555 1555 2.29 LINK O TYR A 171 CA CA A 277 1555 1555 2.32 LINK O ALA A 174 CA CA A 277 1555 1555 2.43 LINK CA CA A 277 O HOH A 332 1555 1555 2.44 CISPEP 1 TYR A 167 PRO A 168 0 3.00 SITE 1 AC1 6 GLN A 2 ASP A 41 LEU A 75 ASN A 77 SITE 2 AC1 6 ILE A 79 VAL A 81 SITE 1 AC2 4 ALA A 169 TYR A 171 ALA A 174 HOH A 332 CRYST1 47.600 62.400 75.800 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 0.021008 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013193 0.00000