HEADER COMPLEX (SERINE PROTEASE/INHIBITOR) 18-DEC-97 1A1Y OBSLTE 12-JUN-00 1A1Y TITLE ALCALASE (SUBTILISIN CARLSBERG VARIANT) IN COMPLEX WITH TITLE 2 CHYMOTRYPSIN INHIBITOR CI-2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALCALASE; COMPND 3 CHAIN: E; COMPND 4 SYNONYM: SUBTILISIN; COMPND 5 EC: 3.4.21.62; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SUBTILISIN-CHYMOTRYPSIN INHIBITOR-2; COMPND 9 CHAIN: I; COMPND 10 SYNONYM: CI-2A INHIBITOR; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HORDEUM VULGARE; SOURCE 5 ORGANISM_COMMON: BARLEY KEYWDS PROTEINASE, SUBTILISIN, COMPLEX (SERINE PROTEASE/INHIBITOR) EXPDTA X-RAY DIFFRACTION AUTHOR W.R.RYPNIEWSKI,C.V.D.OSTEN,P.OESTERGAARD,M.DAUTER,K.S.WILSON REVDAT 3 12-JUN-00 1A1Y 1 OBSLTE REVDAT 2 16-FEB-99 1A1Y 3 SOURCE COMPND REMARK TITLE REVDAT 2 2 3 HETATM DBREF SEQADV JRNL REVDAT 2 3 3 KEYWDS HEADER CONECT LINK REVDAT 2 4 3 ANISOU REVDAT 1 30-DEC-98 1A1Y 0 JRNL AUTH W.R.RYPNIEWSKI,C.V.D.OSTEN,P.OESTERGAARD,M.DAUTER, JRNL AUTH 2 K.S.WILSON JRNL TITL DIRECT OBSERVATION OF CATALYTIC HYDROGEN ATOMS IN JRNL TITL 2 A SERINE PROTEINASE: SUBTILISIN/CI-2A COMPLEX AT JRNL TITL 3 1.05 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.05 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.104 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.104 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.078 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.078 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)) : 95467 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2515 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 553 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2972.11 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2279.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 22 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 27669 REMARK 3 NUMBER OF RESTRAINTS : 32249 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.022 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.129 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.215 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.053 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.034 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.128 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A1Y COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-19) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-1995 REMARK 200 TEMPERATURE (KELVIN) : 277.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DESY-EMBL,HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : MAR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126083 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.46200 REMARK 200 R SYM FOR SHELL (I) : 0.46200 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2SEC, 2CI2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 OE1 GLN I 47 O HOH 537 1.25 REMARK 500 CD GLN I 47 O HOH 537 1.36 REMARK 500 NE2 GLN I 47 O HOH 537 1.63 REMARK 500 OE1 GLN E 137 O HOH 518 2.17 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE E 107 CG1 ILE E 107 CD1 -0.122 REMARK 500 MET E 135 SD MET E 135 CE -0.104 REMARK 500 LYS I 36 CE LYS I 36 NZ 0.110 REMARK 500 ARG I 81 CB ARG I 81 CG -0.112 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE E 8 CB - CG1 - CD1 ANGL. DEV. = 15.3 DEGREES REMARK 500 LYS I 36 CG - CD - CE ANGL. DEV. = 22.5 DEGREES REMARK 500 ARG I 81 CD - NE - CZ ANGL. DEV. = 31.9 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 426 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH 531 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH 540 DISTANCE = 6.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD. REMARK 860 REMARK 860 CORRECTION AFTER RELEASE REMARK 860 DATE: 16-FEB-99 REMARK 860 MODID: 1A1YA REMARK 860 MODIFIED BY: PDB REMARK 860 DESCRIPTION: CONVERTED FROM LAYER 1 OR NDB TO LAYER 2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 NO EXACT MATCHES. THE CLOSEST ARE P00780 AND P01053 REMARK 999 (SWISSPROT). REMARK 999 1A1Y E SWS P00780 1 - 105 NOT IN ATOMS LIST REMARK 999 1A1Y I SWS P01053 1 - 20 NOT IN ATOMS LIST DBREF 1A1Y E 1 275 UNP P00780 SUBT_BACLI 106 379 DBREF 1A1Y I 21 83 UNP P01053 ICI2_HORVU 21 83 SEQADV 1A1Y SER E 103 UNP P00780 THR 207 CONFLICT SEQADV 1A1Y ALA E 129 UNP P00780 PRO 233 CONFLICT SEQADV 1A1Y ASN E 212 UNP P00780 SER 316 CONFLICT SEQADV 1A1Y GLU I 78 UNP P01053 GLN 78 CONFLICT SEQRES 1 E 274 ALA GLN THR VAL PRO TYR GLY ILE PRO LEU ILE LYS ALA SEQRES 2 E 274 ASP LYS VAL GLN ALA GLN GLY PHE LYS GLY ALA ASN VAL SEQRES 3 E 274 LYS VAL ALA VAL LEU ASP THR GLY ILE GLN ALA SER HIS SEQRES 4 E 274 PRO ASP LEU ASN VAL VAL GLY GLY ALA SER PHE VAL ALA SEQRES 5 E 274 GLY GLU ALA TYR ASN THR ASP GLY ASN GLY HIS GLY THR SEQRES 6 E 274 HIS VAL ALA GLY THR VAL ALA ALA LEU ASP ASN THR THR SEQRES 7 E 274 GLY VAL LEU GLY VAL ALA PRO SER VAL SER LEU TYR ALA SEQRES 8 E 274 VAL LYS VAL LEU ASN SER SER GLY SER GLY SER TYR SER SEQRES 9 E 274 GLY ILE VAL SER GLY ILE GLU TRP ALA THR THR ASN GLY SEQRES 10 E 274 MET ASP VAL ILE ASN MET SER LEU GLY GLY ALA SER GLY SEQRES 11 E 274 SER THR ALA MET LYS GLN ALA VAL ASP ASN ALA TYR ALA SEQRES 12 E 274 ARG GLY VAL VAL VAL VAL ALA ALA ALA GLY ASN SER GLY SEQRES 13 E 274 SER SER GLY ASN THR ASN THR ILE GLY TYR PRO ALA LYS SEQRES 14 E 274 TYR ASP SER VAL ILE ALA VAL GLY ALA VAL ASP SER ASN SEQRES 15 E 274 SER ASN ARG ALA SER PHE SER SER VAL GLY ALA GLU LEU SEQRES 16 E 274 GLU VAL MET ALA PRO GLY ALA GLY VAL TYR SER THR TYR SEQRES 17 E 274 PRO THR ASN THR TYR ALA THR LEU ASN GLY THR SER MET SEQRES 18 E 274 ALA SER PRO HIS VAL ALA GLY ALA ALA ALA LEU ILE LEU SEQRES 19 E 274 SER LYS HIS PRO ASN LEU SER ALA SER GLN VAL ARG ASN SEQRES 20 E 274 ARG LEU SER SER THR ALA THR TYR LEU GLY SER SER PHE SEQRES 21 E 274 TYR TYR GLY LYS GLY LEU ILE ASN VAL GLU ALA ALA ALA SEQRES 22 E 274 GLN SEQRES 1 I 63 LYS THR GLU TRP PRO GLU LEU VAL GLY LYS SER VAL GLU SEQRES 2 I 63 GLU ALA LYS LYS VAL ILE LEU GLN ASP LYS PRO GLU ALA SEQRES 3 I 63 GLN ILE ILE VAL LEU PRO VAL GLY THR ILE VAL THR MET SEQRES 4 I 63 GLU TYR ARG ILE ASP ARG VAL ARG LEU PHE VAL ASP LYS SEQRES 5 I 63 LEU ASP ASN ILE ALA GLU VAL PRO ARG VAL GLY HET CA E 276 1 HET CA E 277 1 HET NA E 278 1 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 3 CA 2(CA 2+) FORMUL 5 NA NA 1+ FORMUL 6 HOH *553(H2 O) HELIX 1 1 TYR E 6 LEU E 10 1 5 HELIX 2 2 ALA E 13 ALA E 18 1 6 HELIX 3 3 HIS E 64 ALA E 73 1 10 HELIX 4 4 TYR E 104 THR E 116 1 13 HELIX 5 5 THR E 133 ALA E 144 1 12 HELIX 6 6 THR E 220 LYS E 237 1 18 HELIX 7 7 ALA E 243 SER E 252 1 10 HELIX 8 8 SER E 260 TYR E 263 1 4 HELIX 9 9 VAL E 270 ALA E 273 1 4 HELIX 10 10 PRO I 25 LEU I 27 5 3 HELIX 11 11 VAL I 32 ASP I 42 1 11 SHEET 1 A 7 VAL E 198 PRO E 201 0 SHEET 2 A 7 ILE E 175 VAL E 180 1 N GLY E 178 O VAL E 198 SHEET 3 A 7 VAL E 148 ALA E 152 1 N ALA E 151 O ILE E 175 SHEET 4 A 7 VAL E 121 MET E 124 1 N ILE E 122 O VAL E 148 SHEET 5 A 7 LYS E 27 ASP E 32 1 N ALA E 29 O VAL E 121 SHEET 6 A 7 SER E 89 LYS E 94 1 N SER E 89 O VAL E 28 SHEET 7 A 7 GLY E 46 SER E 49 1 N GLY E 46 O ALA E 92 SHEET 1 B 2 VAL E 205 TYR E 209 0 SHEET 2 B 2 THR E 213 LEU E 217 -1 N LEU E 217 O VAL E 205 SHEET 1 C 2 GLN I 47 PRO I 52 0 SHEET 2 C 2 ARG I 65 VAL I 70 1 N VAL I 66 O GLN I 47 LINK CA CA E 276 O LEU E 75 LINK CA CA E 276 O THR E 79 LINK CA CA E 276 O VAL E 81 LINK CA CA E 277 O HIS E 39 LINK CA CA E 277 O LEU E 42 LINK NA NA E 278 O ALA E 169 LINK NA NA E 278 O TYR E 171 LINK NA NA E 278 O VAL E 174 CISPEP 1 TYR E 167 PRO E 168 0 13.41 CISPEP 2 PRO E 210 THR E 211 0 -5.24 SITE 1 CAT 3 SER E 221 HIS E 64 ASP E 32 CRYST1 45.349 46.783 38.254 78.68 102.96 76.09 P 1 1 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 0.022051 -0.005461 0.006760 0.00000 SCALE2 0.000000 0.022021 -0.006040 0.00000 SCALE3 0.000000 0.000000 0.027815 0.00000