HEADER HYDROLASE/HYDROLASE INHIBITOR 16-SEP-91 2TLD TITLE CRYSTAL STRUCTURE OF AN ENGINEERED SUBTILISIN INHIBITOR COMPLEXED WITH TITLE 2 BOVINE TRYPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN; COMPND 3 CHAIN: E; COMPND 4 EC: 3.4.21.4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: STREPTOMYCES SUBTILISIN INHIBITOR (SSI); COMPND 8 CHAIN: I; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 MOL_ID: 2 KEYWDS PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, TRYPSIN) EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN E, I AUTHOR Y.MITSUI,Y.TAKEUCHI,T.NONAKA,K.T.NAKAMURA REVDAT 4 21-FEB-24 2TLD 1 SEQADV REVDAT 3 24-FEB-09 2TLD 1 VERSN REVDAT 2 01-APR-03 2TLD 1 JRNL REVDAT 1 15-JUL-92 2TLD 0 JRNL AUTH Y.TAKEUCHI,T.NONAKA,K.T.NAKAMURA,S.KOJIMA,K.MIURA,Y.MITSUI JRNL TITL CRYSTAL STRUCTURE OF AN ENGINEERED SUBTILISIN INHIBITOR JRNL TITL 2 COMPLEXED WITH BOVINE TRYPSIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 89 4407 1992 JRNL REFN ISSN 0027-8424 JRNL PMID 1584773 JRNL DOI 10.1073/PNAS.89.10.4407 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.TAKEUCHI,Y.SATOW,K.T.NAKAMURA,Y.MITSUI REMARK 1 TITL REFINED CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' REMARK 1 TITL 2 AND STREPTOMYCES SUBTILISIN INHIBITOR AT 1.8 ANGSTROMS REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 221 309 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6166 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 330 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 4.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2TLD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178679. 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) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-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 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 55.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.40000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.15000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.40000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.15000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.45000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.40000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.15000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.45000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.40000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.15000 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 300 REMARK: SSI IS A DIMERIC MOLECULE (I2) CONSISTING OF TWO IDENTICAL REMARK 300 SUBUNITS. IT BINDS TWO TRYPSIN MOLECULES (2E) TO REMARK 300 FORM A DIMERIC COMPLEX E2I2. THE CRYSTALLOGRAPHIC REMARK 300 ASYMMETRIC UNIT CORRESPONDS TO HALF THE COMPLEX MOLECULE REMARK 300 (EI). IN THIS ENTRY COORDINATES FOR ALPHA-CARBON ATOMS REMARK 300 ARE PROVIDED FOR ONE CHAIN OF TRYPSIN USING THE CHAIN REMARK 300 IDENTIFIER *E* AND FOR ONE CHAIN OF MODIFIED SSI USING REMARK 300 THE CHAIN IDENTIFIER *I*. REMARK 300 REMARK 300 COORDINATES FOR THE OTHER EI COMPLEX CAN BE GENERATED FROM REMARK 300 THE COORDINATES IN THIS ENTRY USING THE FOLLOWING REMARK 300 TRANSFORMATION: REMARK 300 REMARK 300 -1.0 0.0 0.0 REMARK 300 0.0 -1.0 0.0 REMARK 300 0.0 0.0 1.0 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 APPLY THE FOLLOWING TO CHAINS: E, I 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES FORMING THE CATALYTIC TRIAD IN TRYPSIN REMARK 800 REMARK 800 SITE_IDENTIFIER: S13 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: A THREE-RESIDUE POLYPEPTIDE SEGMENT OF REMARK 800 SUBTILISIN CAPABLE OF FORMING AN ANTIPARALLEL BETA SHEET WITH REMARK 800 THE P1, P2 AND P3 RESIDUES OF A LIGAND REMARK 800 REMARK 800 SITE_IDENTIFIER: RAC REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES OF SSI CONNECTED THROUGH A REACTIVE REMARK 800 SITE PEPTIDE BOND (OR A SCISSIBLE BOND) WHICH IS POTENTIALLY REMARK 800 CLEAVED BY TARGET ENZYMES INCLUDING TRYPSIN AND SUBTILISIN. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2SIC RELATED DB: PDB REMARK 900 COMPLEX OF SUBTILISIN BPN WITH WILD STRETOMYCES SUBTILISIN INHIBITOR REMARK 900 RELATED ID: 3SIC RELATED DB: PDB DBREF 2TLD E 16 245 UNP P00760 TRY1_BOVIN 21 243 DBREF 2TLD I 4 113 UNP P01006 SSI_STRAO 35 144 SEQADV 2TLD E UNP P00760 TYR 185 DELETION SEQADV 2TLD E UNP P00760 LYS 190 DELETION SEQADV 2TLD E UNP P00760 GLN 219 DELETION SEQADV 2TLD GLY I 70 UNP P01006 MET 101 CONFLICT SEQADV 2TLD LYS I 73 UNP P01006 MET 104 CONFLICT SEQRES 1 E 220 ILE VAL GLY GLY TYR THR CYS GLY ALA ASN THR VAL PRO SEQRES 2 E 220 TYR GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 E 220 GLY SER LEU ILE ASN SER GLN TRP VAL VAL SER ALA ALA SEQRES 4 E 220 HIS CYS TYR LYS SER GLY ILE GLN VAL ARG LEU GLY GLU SEQRES 5 E 220 ASP ASN ILE ASN VAL VAL GLU GLY ASN GLU GLN PHE ILE SEQRES 6 E 220 SER ALA SER LYS SER ILE VAL HIS PRO SER TYR ASN SER SEQRES 7 E 220 ASN THR LEU ASN ASN ASP ILE MET LEU ILE LYS LEU LYS SEQRES 8 E 220 SER ALA ALA SER LEU ASN SER ARG VAL ALA SER ILE SER SEQRES 9 E 220 LEU PRO THR SER CYS ALA SER ALA GLY THR GLN CYS LEU SEQRES 10 E 220 ILE SER GLY TRP GLY ASN THR LYS SER SER GLY THR SER SEQRES 11 E 220 TYR PRO ASP VAL LEU LYS CYS LEU LYS ALA PRO ILE LEU SEQRES 12 E 220 SER ASP SER SER CYS LYS SER ALA TYR PRO GLY GLN ILE SEQRES 13 E 220 THR SER ASN MET PHE CYS ALA GLY LEU GLU GLY GLY ASP SEQRES 14 E 220 SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL CYS SER SEQRES 15 E 220 GLY LYS LEU GLN GLY ILE VAL SER TRP GLY SER GLY CYS SEQRES 16 E 220 ALA LYS ASN LYS PRO GLY VAL TYR THR LYS VAL CYS ASN SEQRES 17 E 220 TYR VAL SER TRP ILE LYS GLN THR ILE ALA SER ASN SEQRES 1 I 110 SER ALA LEU TYR ALA PRO SER ALA LEU VAL LEU THR VAL SEQRES 2 I 110 GLY LYS GLY VAL SER ALA THR THR ALA ALA PRO GLU ARG SEQRES 3 I 110 ALA VAL THR LEU THR CYS ALA PRO GLY PRO SER GLY THR SEQRES 4 I 110 HIS PRO ALA ALA GLY SER ALA CYS ALA ASP LEU ALA ALA SEQRES 5 I 110 VAL GLY GLY ASP LEU ASN ALA LEU THR ARG GLY GLU ASP SEQRES 6 I 110 VAL GLY CYS PRO LYS VAL TYR ASP PRO VAL LEU LEU THR SEQRES 7 I 110 VAL ASP GLY VAL TRP GLN GLY LYS ARG VAL SER TYR GLU SEQRES 8 I 110 ARG VAL PHE SER ASN GLU CYS GLU MET ASN ALA HIS GLY SEQRES 9 I 110 SER SER VAL PHE ALA PHE HELIX 1 H1 SER E 164 TYR E 172 1SINGLE ALPHA TURN,REST IRREG. 9 HELIX 2 H2 LYS E 230 VAL E 235 5CONTIGUOUS WITH H3 6 HELIX 3 H3 SER E 236 ASN E 245 1CONTIGUOUS WITH H2 10 HELIX 4 H4 ALA I 46 VAL I 56 1 11 HELIX 5 H5 ASN I 99 HIS I 106 1 8 SHEET 1 S1 6 LYS E 156 PRO E 161 0 SHEET 2 S1 6 CYS E 136 GLY E 140 -1 SHEET 3 S1 6 GLY E 197 CYS E 201 -1 SHEET 4 S1 6 LYS E 204 TRP E 215 -1 SHEET 5 S1 6 GLY E 226 VAL E 231 -1 SHEET 6 S1 6 ASN E 179 ALA E 183 -1 SHEET 1 S2 4 GLY E 43 SER E 45 0 SHEET 2 S2 4 VAL E 52 ALA E 55 -1 SHEET 3 S2 4 ILE E 103 LYS E 107 -1 SHEET 4 S2 4 LYS E 87 HIS E 91 -1 SHEET 1 S3 2 ILE E 63 LEU E 67 0 SHEET 2 S3 2 GLN E 81 ALA E 85 -1 SHEET 1 S4 5 SER I 40 THR I 42 0 SHEET 2 S4 5 ARG I 29 CYS I 35 -1 SHEET 3 S4 5 SER I 10 GLY I 19 -1 SHEET 4 S4 5 PRO I 77 GLN I 87 -1 SHEET 5 S4 5 LYS I 89 PHE I 97 -1 SITE 1 CAT 3 ASP E 102 HIS E 57 SER E 195 SITE 1 S13 3 SER E 214 TRP E 215 GLY E 216 SITE 1 RAC 2 LYS I 73 VAL I 74 CRYST1 110.900 116.800 64.300 90.00 90.00 90.00 I 2 2 2 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 0.009017 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015552 0.00000