PDB Short entry for 4PTI HEADER PROTEINASE INHIBITOR (TRYPSIN) 27-SEP-82 4PTI TITLE THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS TITLE 2 IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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 R.HUBER,D.KUKLA,A.RUEHLMANN,O.EPP,H.FORMANEK,J.DEISENHOFER, AUTHOR 2 W.STEIGEMANN REVDAT 7 24-FEB-09 4PTI 1 VERSN REVDAT 6 16-APR-87 4PTI 1 SOURCE REMARK REVDAT 5 31-MAY-84 4PTI 1 REMARK REVDAT 4 23-FEB-84 4PTI 1 JRNL REVDAT 3 31-JAN-84 4PTI 1 REMARK REVDAT 2 30-SEP-83 4PTI 1 REVDAT REVDAT 1 18-JAN-83 4PTI 0 SPRSDE 18-JAN-83 4PTI 3PTI JRNL AUTH M.MARQUART,J.WALTER,J.DEISENHOFER,W.BODE,R.HUBER JRNL TITL THE GEOMETRY OF THE REACTIVE SITE AND OF THE JRNL TITL 2 PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS JRNL TITL 3 COMPLEXES WITH INHIBITORS JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 39 480 1983 JRNL REFN ISSN 0108-7681 REMARK 1 REMARK 1 REFERENCE 1 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 2 REMARK 1 AUTH J.DEISENHOFER,W.STEIGEMANN REMARK 1 TITL CRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF REMARK 1 TITL 2 BOVINE PANCREATIC TRYPSIN INHIBITOR AT 1.5 REMARK 1 TITL 3 ANGSTROMS RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 31 238 1975 REMARK 1 REFN ISSN 0108-7681 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.DEISENHOFER,W.STEIGEMANN REMARK 1 TITL THE MODEL OF THE BASIC PANCREATIC TRYPSIN REMARK 1 TITL 2 INHIBITOR REFINED AT 1.5 ANGSTROMS RESOLUTION REMARK 1 REF BAYER SYMP. V. 5 484 1974 REMARK 1 REFN ISSN 0067-4672 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.HUBER,D.KUKLA,A.RUEHLMANN,W.STEIGEMANN REMARK 1 TITL PANCREATIC TRYPSIN INHIBITOR (KUNITZ). PART I. REMARK 1 TITL 2 STRUCTURE AND FUNCTION REMARK 1 REF COLD SPRING HARBOR V. 36 141 1972 REMARK 1 REF 2 SYMP.QUANT.BIOL. REMARK 1 REFN ISSN 0091-7451 REMARK 1 REFERENCE 5 REMARK 1 AUTH A.RUEHLMANN,H.J.SCHRAMM,D.KUKLA,R.HUBER REMARK 1 TITL PANCREATIC TRYPSIN INHIBITOR (KUNITZ). PART II. REMARK 1 TITL 2 COMPLEXES WITH PROTEINASES REMARK 1 REF COLD SPRING HARBOR V. 36 148 1972 REMARK 1 REF 2 SYMP.QUANT.BIOL. REMARK 1 REFN ISSN 0091-7451 REMARK 1 REFERENCE 6 REMARK 1 AUTH R.HUBER,D.KUKLA,A.RUEHLMANN,O.EPP,H.FORMANEK REMARK 1 TITL THE BASIC TRYPSIN INHIBITOR OF BOVINE PANCREAS. I. REMARK 1 TITL 2 STRUCTURE ANALYSIS AND CONFORMATION OF THE REMARK 1 TITL 3 POLYPEPTIDE CHAIN REMARK 1 REF NATURWISSENSCHAFTEN V. 57 389 1970 REMARK 1 REFN ISSN 0028-1042 REMARK 1 REFERENCE 7 REMARK 1 EDIT M.O.DAYHOFF REMARK 1 REF ATLAS OF PROTEIN SEQUENCE V. 5 88 1973 REMARK 1 REF 2 AND STRUCTURE,SUPPLEMENT 1 REMARK 1 PUBL NATIONAL BIOMEDICAL RESEARCH FOUNDATION, SILVER REMARK 1 PUBL 2 SPRING,MD. REMARK 1 REFN ISSN 0-912466-04-9 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 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 : 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 SET) : 0.162 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 : 454 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 60 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 4PTI 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 (%): 33.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 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 21.55000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.55000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 11.45000 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 1 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 GLU A 7 OE1 - CD - OE2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 17 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 TYR A 35 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 5.0 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 ASN A 44 102.13 -162.55 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 GLU A 7 0.10 SIDE_CHAIN REMARK 500 ASN A 44 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 124 DISTANCE = 5.64 ANGSTROMS DBREF 4PTI 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 FORMUL 2 HOH *60(H2 O) HELIX 1 H1 SER A 47 GLY A 56 1 10 SHEET 1 S1 2 ALA A 16 ALA A 25 0 SHEET 2 S1 2 GLY A 28 GLY A 36 -1 SSBOND 1 CYS A 5 CYS A 55 1555 1555 2.05 SSBOND 2 CYS A 14 CYS A 38 1555 1555 2.09 SSBOND 3 CYS A 30 CYS A 51 1555 1555 2.02 CRYST1 43.100 22.900 48.600 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 0.023202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.043668 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020576 0.00000