HEADER PROTEINASE INHIBITOR (TRYPSIN) 18-FEB-95 1BPI TITLE THE STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR AT TITLE 2 125K: DEFINITION OF CARBOXYL-TERMINAL RESIDUES GLYCINE-57 TITLE 3 AND ALANINE-58 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BOVINE PANCREATIC TRYPSIN INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS PROTEINASE INHIBITOR (TRYPSIN) EXPDTA X-RAY DIFFRACTION AUTHOR S.PARKIN,B.RUPP,H.HOPE REVDAT 2 24-FEB-09 1BPI 1 VERSN REVDAT 1 03-JUN-95 1BPI 0 JRNL AUTH S.PARKIN,B.RUPP,H.HOPE JRNL TITL STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR JRNL TITL 2 AT 125 K DEFINITION OF CARBOXYL-TERMINAL RESIDUES JRNL TITL 3 GLY57 AND ALA58. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 52 18 1996 JRNL REFN ISSN 0907-4449 JRNL PMID 15299722 JRNL DOI 10.1107/S0907444995008675 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-93, XFIT REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.187 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)) : 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 : 460 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 166 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 : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES GLU 7 AND ARG 53 WERE REMARK 3 MODELED IN TWO CONFORMATIONS. 145.6 WATER MOLECULES OVER 167 REMARK 3 SITES WERE MODELED. 123 ARE AT FULL OCCUPANCY, 39 ARE AT HALF REMARK 3 OCCUPANCY AND THE REMAINDER HAVE OCCUPANCIES DETERMINED BY THE REMARK 3 DISORDER AT RESIDUES GLU 7 AND ARG 53. THE PHOSPHATE WAS REMARK 3 MODELED IN TWO CONFORMATIONS. RESTRAINED ANISOTROPIC THERMAL REMARK 3 PARAMETERS WERE REFINED. THE COORDINATES IN THIS ENTRY ARE REMARK 3 THOSE OF THE ISOTROPIC MODEL. R VALUES FOR THE ISOTROPIC AND REMARK 3 ANISOTROPIC MODELS WERE 0.187 AND 0.161 FOR ALL DATA. FREE R REMARK 3 VALUES FOR BOTH MODELS WERE INSIGNIFICANTLY DIFFERENT. PROTEIN REMARK 3 GEOMETRY FOR MAJOR AND MINOR CONFORMATIONS OF GLU 7 AND ASP 53 REMARK 3 WAS CHECKED WITH THE PROCHECK PROGRAM (LASKOWSKI, MACARTHUR, REMARK 3 MOSS, THORNTON (1993) J. APPL. CRYST. 26, 283 - 291). THE REMARK 3 OMEGA TORSION ANGLE OF ARG 1 SHOWS A MARKED DEVIATION FROM REMARK 3 PLANARITY. ELECTRON DENSITY MAPS CLEARLY SUPPORT THIS REMARK 3 DISTORTION. REMARK 4 REMARK 4 1BPI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-84 REMARK 200 TEMPERATURE (KELVIN) : 125 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SIEMENS XDISK 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: SHELXL-93 REMARK 200 STARTING MODEL: NULL 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: 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 37.69500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.29050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.69500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 11.29050 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 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 3 CG ASP A 3 OD2 0.181 REMARK 500 GLU A 7 CD GLU A 7 OE1 0.169 REMARK 500 GLU A 7 CD GLU A 7 OE2 0.172 REMARK 500 GLU A 49 CD GLU A 49 OE2 0.160 REMARK 500 ASP A 50 CG ASP A 50 OD2 0.172 REMARK 500 REMARK 500 REMARK: NULL 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 1 O - C - N ANGL. DEV. = -11.6 DEGREES REMARK 500 ASP A 3 CB - CG - OD1 ANGL. DEV. = 9.6 DEGREES REMARK 500 GLU A 7 OE1 - CD - OE2 ANGL. DEV. = -7.3 DEGREES REMARK 500 GLU A 7 OE1 - CD - OE2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 17 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 42 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 50 CB - CG - OD1 ANGL. DEV. = 8.0 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 PRO A 2 144.88 -34.51 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 ARG A 39 0.12 SIDE_CHAIN REMARK 500 ARG A 42 0.10 SIDE_CHAIN REMARK 500 ARG A 53 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 90 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 103 DISTANCE = 5.54 ANGSTROMS REMARK 525 HOH A 123 DISTANCE = 6.73 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 INITIAL MODEL DERIVED FROM THE COORDINATE SET OF PDB ENTRY REMARK 600 5PTI. PRIOR TO REFINEMENT THE MODEL WAS MODIFIED AS REMARK 600 FOLLOWS: (I) DISORDER WAS REMOVED, MAJOR CONFORMATIONS REMARK 600 INCLUDED AT FULL OCCUPANCY. (II) HYDROGEN ATOMS REMOVED. REMARK 600 (III) ISOTROPIC THERMAL PARAMETERS HALVED, CONVERTED TO *U* REMARK 600 FORMAT AND ROUNDED TO THE NEAREST 0.01 ANGSTROM SQUARED. REMARK 600 (IV) AMINO ACID GEOMETRIES RESTRAINED ACCORDING TO ENGH AND REMARK 600 HUBER (1991), ACTA CRYST. A47 PP.392-400. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 59 DBREF 1BPI A 1 58 UNP P00974 BPT1_BOVIN 36 93 SEQRES 1 A 58 ARG PRO ASP PHE CYS LEU GLU PRO PRO TYR THR GLY PRO SEQRES 2 A 58 CYS LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA LYS SEQRES 3 A 58 ALA GLY LEU CYS GLN THR PHE VAL TYR GLY GLY CYS ARG SEQRES 4 A 58 ALA LYS ARG ASN ASN PHE LYS SER ALA GLU ASP CYS MET SEQRES 5 A 58 ARG THR CYS GLY GLY ALA HET PO4 A 59 10 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *167(H2 O) HELIX 1 H1 PRO A 2 GLU A 7 5 6 HELIX 2 H2 SER A 47 GLY A 56 1 10 SHEET 1 S1 3 LEU A 29 TYR A 35 0 SHEET 2 S1 3 ILE A 18 ASN A 24 -1 SHEET 3 S1 3 PHE A 45 PHE A 45 -1 SSBOND 1 CYS A 5 CYS A 55 1555 1555 2.01 SSBOND 2 CYS A 14 CYS A 38 1555 1555 2.03 SSBOND 3 CYS A 30 CYS A 51 1555 1555 2.02 SITE 1 AC1 19 ARG A 1 LYS A 15 ARG A 20 TYR A 35 SITE 2 AC1 19 LYS A 41 LYS A 46 ALA A 58 HOH A 135 SITE 3 AC1 19 HOH A 142 HOH A 146 HOH A 151 HOH A 167 SITE 4 AC1 19 HOH A 192 HOH A 194 HOH A 195 HOH A 196 SITE 5 AC1 19 HOH A 197 HOH A 214 HOH A 215 CRYST1 75.390 22.581 28.600 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 0.013264 0.000000 0.000000 0.00000 SCALE2 0.000000 0.044285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034965 0.00000