HEADER HYDROLASE 15-FEB-07 2EEK TITLE CRYSTAL STRUCTURE OF ATLANTIC COD TRYPSIN COMPLEXED WITH BENZAMIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PEPTIDASE S1; COMPND 5 SYNONYM: TRYPSIN I, TRYPSIN; COMPND 6 EC: 3.4.21.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GADUS MORHUA; SOURCE 3 ORGANISM_COMMON: ATLANTIC COD; SOURCE 4 ORGANISM_TAXID: 8049 KEYWDS BENZAMIDINE INHIBITED, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.IYAGUCHI,E.TOYOTA REVDAT 3 25-OCT-23 2EEK 1 REMARK REVDAT 2 24-FEB-09 2EEK 1 VERSN REVDAT 1 19-FEB-08 2EEK 0 JRNL AUTH D.IYAGUCHI,E.TOYOTA JRNL TITL CRYSTAL STRUCTURE OF ATLANTIC COD TRYPSIN COMPLEXED WITH JRNL TITL 2 BENZAMIDINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 15584 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1573 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 260 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1645 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -3.82000 REMARK 3 B33 (A**2) : 4.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.369 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 2EEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000026567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15584 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07900 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) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1MBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, HEPES, PH 7.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293.0K 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 23.60650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.86800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.59200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.86800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.60650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.59200 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: 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 GLN A 27 65.72 -112.18 REMARK 500 SER A 37 42.62 -140.77 REMARK 500 HIS A 71 -60.11 -130.41 REMARK 500 ASN A 115 -159.44 -155.64 REMARK 500 ALA A 133 -6.97 83.78 REMARK 500 ASP A 189 166.28 179.96 REMARK 500 SER A 214 -71.52 -108.50 REMARK 500 REMARK 500 REMARK: NULL 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 301 DBREF 2EEK A 16 243 UNP P16049 TRY1_GADMO 20 239 SEQRES 1 A 220 ILE VAL GLY GLY TYR GLU CYS THR LYS HIS SER GLN ALA SEQRES 2 A 220 HIS GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 A 220 GLY SER LEU VAL SER LYS ASP TRP VAL VAL SER ALA ALA SEQRES 4 A 220 HIS CYS TYR LYS SER VAL LEU ARG VAL ARG LEU GLY GLU SEQRES 5 A 220 HIS HIS ILE ARG VAL ASN GLU GLY THR GLU GLN TYR ILE SEQRES 6 A 220 SER SER SER SER VAL ILE ARG HIS PRO ASN TYR SER SER SEQRES 7 A 220 TYR ASN ILE ASN ASN ASP ILE MET LEU ILE LYS LEU THR SEQRES 8 A 220 LYS PRO ALA THR LEU ASN GLN TYR VAL HIS ALA VAL ALA SEQRES 9 A 220 LEU PRO THR GLU CYS ALA ALA ASP ALA THR MET CYS THR SEQRES 10 A 220 VAL SER GLY TRP GLY ASN THR MET SER SER VAL ALA ASP SEQRES 11 A 220 GLY ASP LYS LEU GLN CYS LEU SER LEU PRO ILE LEU SER SEQRES 12 A 220 HIS ALA ASP CYS ALA ASN SER TYR PRO GLY MET ILE THR SEQRES 13 A 220 GLN SER MET PHE CYS ALA GLY TYR LEU GLU GLY GLY LYS SEQRES 14 A 220 ASP SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL CYS SEQRES 15 A 220 ASN GLY VAL LEU GLN GLY VAL VAL SER TRP GLY TYR GLY SEQRES 16 A 220 CYS ALA GLU ARG ASP HIS PRO GLY VAL TYR ALA LYS VAL SEQRES 17 A 220 CYS VAL LEU SER GLY TRP VAL ARG ASP THR MET ALA HET CA A 401 1 HET NA A 501 1 HET BEN A 301 9 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM BEN BENZAMIDINE FORMUL 2 CA CA 2+ FORMUL 3 NA NA 1+ FORMUL 4 BEN C7 H8 N2 FORMUL 5 HOH *119(H2 O) HELIX 1 1 ALA A 55 TYR A 59 5 5 HELIX 2 2 SER A 164 TYR A 172 1 9 HELIX 3 3 VAL A 231 ALA A 243 1 13 SHEET 1 A 7 TYR A 20 GLU A 21 0 SHEET 2 A 7 GLN A 156 PRO A 161 -1 O CYS A 157 N TYR A 20 SHEET 3 A 7 MET A 135 GLY A 140 -1 N CYS A 136 O LEU A 160 SHEET 4 A 7 PRO A 198 CYS A 201 -1 O VAL A 200 N THR A 137 SHEET 5 A 7 VAL A 204 TRP A 215 -1 O VAL A 204 N CYS A 201 SHEET 6 A 7 GLY A 226 LYS A 230 -1 O VAL A 227 N TRP A 215 SHEET 7 A 7 MET A 180 ALA A 183 -1 N PHE A 181 O TYR A 228 SHEET 1 B 7 GLN A 30 ASN A 34 0 SHEET 2 B 7 HIS A 40 LEU A 46 -1 O CYS A 42 N LEU A 33 SHEET 3 B 7 TRP A 51 SER A 54 -1 O VAL A 53 N SER A 45 SHEET 4 B 7 MET A 104 LEU A 108 -1 O ILE A 106 N VAL A 52 SHEET 5 B 7 GLN A 81 ARG A 90 -1 N ILE A 89 O LEU A 105 SHEET 6 B 7 ARG A 64 LEU A 67 -1 N LEU A 67 O GLN A 81 SHEET 7 B 7 GLN A 30 ASN A 34 -1 N ASN A 34 O ARG A 64 SSBOND 1 CYS A 22 CYS A 157 1555 1555 2.03 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 3 CYS A 128 CYS A 232 1555 1555 2.03 SSBOND 4 CYS A 136 CYS A 201 1555 1555 2.03 SSBOND 5 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 6 CYS A 191 CYS A 220 1555 1555 2.03 SITE 1 AC1 6 GLU A 70 HIS A 72 VAL A 75 GLU A 77 SITE 2 AC1 6 GLU A 80 HOH A 594 SITE 1 AC2 1 ARG A 90 SITE 1 AC3 7 ASP A 189 SER A 190 GLN A 192 SER A 195 SITE 2 AC3 7 VAL A 213 GLY A 219 GLY A 226 CRYST1 47.213 59.184 63.736 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 0.021181 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016896 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015690 0.00000