PDB Short entry for 1S0R HEADER HYDROLASE 02-JAN-04 1S0R TITLE BOVINE PANCREATIC TRYPSIN INHIBITED WITH BENZAMIDINE AT ATOMIC TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSINOGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRYPSIN; COMPND 5 SYNONYM: BETA-TRYPSIN; COMPND 6 EC: 3.4.21.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS TRYPSIN, BENZAMIDINE, ATOMIC RESOLUTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CHAMORRO GAVILANES,S.GARCA-GRANDA REVDAT 4 23-AUG-23 1S0R 1 REMARK LINK REVDAT 3 31-JAN-18 1S0R 1 REMARK REVDAT 2 24-FEB-09 1S0R 1 VERSN REVDAT 1 18-JAN-05 1S0R 0 JRNL AUTH J.A.CHAMORRO,J.A.CUESTA-SEIJO,S.GARCA-GRANDA JRNL TITL PANCRATIC BOVINE TRYPSIN NATIVE AND INHIBITED WITH JRNL TITL 2 BENZAMIDINE FROM SYNCHOTRON DATA. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.02 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.111 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.111 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4963 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 99328 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.098 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.098 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.125 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3972 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 75970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1629 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1973.9 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1599.9 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 18027 REMARK 3 NUMBER OF RESTRAINTS : 21495 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.033 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.088 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.096 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.095 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) REMARK 4 REMARK 4 1S0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021221. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.02 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94365 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 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) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.8 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1S0Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, BENZAMIDINE, AMONUM REMARK 280 SULPHATE, CALCIUM CHLORIDE, TRIS-HCL, PH 8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 100K 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 27.19650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.27100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.21200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.27100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.19650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.21200 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 99 NE - CZ - NH1 ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 GLY A 128 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 GLU A 167 OE1 - CD - OE2 ANGL. DEV. = 9.6 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 ASP A 53 -83.56 -120.49 REMARK 500 SER A 126 -76.00 -52.05 REMARK 500 SER A 127 66.20 -171.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 224 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 ASN A 54 O 91.6 REMARK 620 3 VAL A 57 O 165.5 80.7 REMARK 620 4 GLU A 62 OE2 102.5 159.3 88.3 REMARK 620 5 HOH A 227 O 86.4 89.6 105.6 76.5 REMARK 620 6 HOH A 235 O 79.5 103.6 90.4 93.9 160.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 225 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J8A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BENZAMIDINE INHIBITED BOVINE PANCREATIC REMARK 900 TRYPSIN AT 105K TO 1.21A RESOLUTION FROM LABORATORY SOURCE WITH REMARK 900 HIGH NUMBER OF WATERS MODELLED REMARK 900 RELATED ID: 1S0Q RELATED DB: PDB REMARK 900 NATIVE BOVINE PANCREATIC TRYPSIN DBREF 1S0R A 1 223 UNP P00760 TRY1_BOVIN 21 243 SEQRES 1 A 223 ILE VAL GLY GLY TYR THR CYS GLY ALA ASN THR VAL PRO SEQRES 2 A 223 TYR GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 A 223 GLY SER LEU ILE ASN SER GLN TRP VAL VAL SER ALA ALA SEQRES 4 A 223 HIS CYS TYR LYS SER GLY ILE GLN VAL ARG LEU GLY GLU SEQRES 5 A 223 ASP ASN ILE ASN VAL VAL GLU GLY ASN GLU GLN PHE ILE SEQRES 6 A 223 SER ALA SER LYS SER ILE VAL HIS PRO SER TYR ASN SER SEQRES 7 A 223 ASN THR LEU ASN ASN ASP ILE MET LEU ILE LYS LEU LYS SEQRES 8 A 223 SER ALA ALA SER LEU ASN SER ARG VAL ALA SER ILE SER SEQRES 9 A 223 LEU PRO THR SER CYS ALA SER ALA GLY THR GLN CYS LEU SEQRES 10 A 223 ILE SER GLY TRP GLY ASN THR LYS SER SER GLY THR SER SEQRES 11 A 223 TYR PRO ASP VAL LEU LYS CYS LEU LYS ALA PRO ILE LEU SEQRES 12 A 223 SER ASP SER SER CYS LYS SER ALA TYR PRO GLY GLN ILE SEQRES 13 A 223 THR SER ASN MET PHE CYS ALA GLY TYR LEU GLU GLY GLY SEQRES 14 A 223 LYS ASP SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL SEQRES 15 A 223 CYS SER GLY LYS LEU GLN GLY ILE VAL SER TRP GLY SER SEQRES 16 A 223 GLY CYS ALA GLN LYS ASN LYS PRO GLY VAL TYR THR LYS SEQRES 17 A 223 VAL CYS ASN TYR VAL SER TRP ILE LYS GLN THR ILE ALA SEQRES 18 A 223 SER ASN HET CA A 224 1 HET BEN A 225 9 HETNAM CA CALCIUM ION HETNAM BEN BENZAMIDINE FORMUL 2 CA CA 2+ FORMUL 3 BEN C7 H8 N2 FORMUL 4 HOH *335(H2 O) HELIX 1 1 ALA A 38 TYR A 42 5 5 HELIX 2 2 SER A 144 TYR A 152 1 9 HELIX 3 3 TYR A 212 SER A 222 1 11 SHEET 1 A 7 TYR A 5 THR A 6 0 SHEET 2 A 7 LYS A 136 PRO A 141 -1 O CYS A 137 N TYR A 5 SHEET 3 A 7 GLN A 115 GLY A 120 -1 N ILE A 118 O LEU A 138 SHEET 4 A 7 PRO A 180 CYS A 183 -1 O VAL A 182 N LEU A 117 SHEET 5 A 7 LYS A 186 TRP A 193 -1 O LYS A 186 N CYS A 183 SHEET 6 A 7 GLY A 204 LYS A 208 -1 O VAL A 205 N TRP A 193 SHEET 7 A 7 MET A 160 ALA A 163 -1 N PHE A 161 O TYR A 206 SHEET 1 B 7 GLN A 15 ASN A 19 0 SHEET 2 B 7 HIS A 23 ASN A 31 -1 O CYS A 25 N LEU A 18 SHEET 3 B 7 TRP A 34 SER A 37 -1 O VAL A 36 N SER A 28 SHEET 4 B 7 MET A 86 LEU A 90 -1 O MET A 86 N SER A 37 SHEET 5 B 7 GLN A 63 VAL A 72 -1 N LYS A 69 O LYS A 89 SHEET 6 B 7 GLN A 47 LEU A 50 -1 N LEU A 50 O GLN A 63 SHEET 7 B 7 GLN A 15 ASN A 19 -1 N SER A 17 O ARG A 49 SSBOND 1 CYS A 7 CYS A 137 1555 1555 2.04 SSBOND 2 CYS A 25 CYS A 41 1555 1555 2.04 SSBOND 3 CYS A 109 CYS A 210 1555 1555 2.01 SSBOND 4 CYS A 116 CYS A 183 1555 1555 2.00 SSBOND 5 CYS A 148 CYS A 162 1555 1555 2.02 SSBOND 6 CYS A 173 CYS A 197 1555 1555 2.02 LINK OE1 GLU A 52 CA CA A 224 1555 1555 2.26 LINK O ASN A 54 CA CA A 224 1555 1555 2.31 LINK O VAL A 57 CA CA A 224 1555 1555 2.29 LINK OE2 GLU A 62 CA CA A 224 1555 1555 2.33 LINK CA CA A 224 O HOH A 227 1555 1555 2.37 LINK CA CA A 224 O HOH A 235 1555 1555 2.34 CISPEP 1 SER A 127 GLY A 128 0 9.09 SITE 1 AC1 6 GLU A 52 ASN A 54 VAL A 57 GLU A 62 SITE 2 AC1 6 HOH A 227 HOH A 235 SITE 1 AC2 7 ASP A 171 SER A 172 GLY A 194 GLY A 196 SITE 2 AC2 7 CYS A 197 GLY A 204 HOH A 254 CRYST1 54.393 58.424 66.542 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 0.018385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015028 0.00000