PDB Short entry for 8PTI HEADER PROTEINASE INHIBITOR (TRYPSIN) 17-DEC-90 8PTI TITLE CRYSTAL STRUCTURE OF A Y35G MUTANT OF BOVINE PANCREATIC TITLE 2 TRYPSIN INHIBITOR 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 D.HOUSSET,K.-S.KIM,J.FUCHS,C.WOODWARD,A.WLODAWER REVDAT 3 24-FEB-09 8PTI 1 VERSN REVDAT 2 15-OCT-91 8PTI 1 REMARK REVDAT 1 15-APR-91 8PTI 0 JRNL AUTH D.HOUSSET,K.S.KIM,J.FUCHS,C.WOODWARD,A.WLODAWER JRNL TITL CRYSTAL STRUCTURE OF A Y35G MUTANT OF BOVINE JRNL TITL 2 PANCREATIC TRYPSIN INHIBITOR. JRNL REF J.MOL.BIOL. V. 220 757 1991 JRNL REFN ISSN 0022-2836 JRNL PMID 1714504 JRNL DOI 10.1016/0022-2836(91)90115-M REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.EIGENBROT,M.RANDAL,A.A.KOSSIAKOFF REMARK 1 TITL STRUCTURAL EFFECTS INDUCED BY REMOVAL OF A REMARK 1 TITL 2 DISULFIDE-BRIDGE. THE X-RAY STRUCTURE OF THE REMARK 1 TITL 3 C30A(SLASH)C51A MUTANT OF BASIC PANCREATIC TRYPSIN REMARK 1 TITL 4 INHIBITOR AT 1.6 ANGSTROMS REMARK 1 REF PROTEIN ENG. V. 3 591 1990 REMARK 1 REFN ISSN 0269-2139 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.R.HYNES,M.RANDAL,L.A.KENNEDY,C.EIGENBROT, REMARK 1 AUTH 2 A.A.KOSSIAKOFF REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF THE PROTEASE INHIBITOR REMARK 1 TITL 2 DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN REMARK 1 TITL 3 PRECURSOR REMARK 1 REF BIOCHEMISTRY V. 29 10018 1990 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.WLODAWER,J.NACHMAN,G.L.GILLILAND,W.GALLAGHER, REMARK 1 AUTH 2 C.WOODWARD REMARK 1 TITL STRUCTURE OF FORM III CRYSTALS OF BOVINE REMARK 1 TITL 2 PANCREATIC TRYPSIN INHIBITOR. REMARK 1 REF J.MOL.BIOL. V. 198 469 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.WLODAWER,J.WALTER,R.HUBER,L.SJOLIN REMARK 1 TITL STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR. REMARK 1 TITL 2 RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT OF REMARK 1 TITL 3 CRYSTAL FORM II REMARK 1 REF J.MOL.BIOL. V. 180 307 1984 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 5 REMARK 1 AUTH A.WLODAWER,J.DEISENHOFER,R.HUBER REMARK 1 TITL COMPARISON OF TWO HIGHLY REFINED STRUCTURES OF REMARK 1 TITL 2 BOVINE PANCREATIC TRYPSIN INHIBITOR REMARK 1 REF J.MOL.BIOL. V. 193 145 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 6 REMARK 1 AUTH J.WALTER,R.HUBER REMARK 1 TITL PANCREATIC TRYPSIN INHIBITOR. A NEW CRYSTAL FORM REMARK 1 TITL 2 AND ITS ANALYSIS REMARK 1 REF J.MOL.BIOL. V. 167 911 1983 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL 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 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 70 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.020 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8PTI 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 : 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 <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: 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 (%): 42.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 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 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 23.37500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.30500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.37500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.37500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.30500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.37500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.37500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.30500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.37500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.37500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.30500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 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 205 LIES ON A SPECIAL POSITION. 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 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 1 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 3 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 39 NE - CZ - NH2 ANGL. DEV. = -3.6 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 ALA A 40 54.25 -147.85 REMARK 500 ARG A 42 -140.55 58.84 REMARK 500 ASN A 44 112.47 -162.25 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 337 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 363 DISTANCE = 5.22 ANGSTROMS DBREF 8PTI A 1 58 UNP P00974 BPT1_BOVIN 36 93 SEQADV 8PTI GLY A 35 UNP P00974 TYR 70 CONFLICT 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 GLY 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 FORMUL 2 HOH *70(H2 O) HELIX 1 H1 PRO A 2 GLU A 7 5ALL DONORS,ACCEPTORS INCLUDED 6 HELIX 2 H2 SER A 47 GLY A 56 1ALL DONORS,ACCEPTORS INCLUDED 10 SHEET 1 S1 3 LEU A 29 GLY A 35 0 SHEET 2 S1 3 ILE A 18 ASN A 24 -1 N ILE A 18 O GLY A 35 SHEET 3 S1 3 PHE A 45 PHE A 45 -1 N PHE A 45 O TYR A 21 SSBOND 1 CYS A 5 CYS A 55 1555 1555 1.99 SSBOND 2 CYS A 14 CYS A 38 1555 1555 2.03 SSBOND 3 CYS A 30 CYS A 51 1555 1555 2.03 CRYST1 46.750 46.750 50.610 90.00 90.00 90.00 P 42 21 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 0.021390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019759 0.00000