HEADER HYDROLASE 03-AUG-02 1MBQ TITLE ANIONIC TRYPSIN FROM PACIFIC CHUM SALMON COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ONCORHYNCHUS KETA; SOURCE 3 ORGANISM_COMMON: CHUM SALMON; SOURCE 4 ORGANISM_TAXID: 8018; SOURCE 5 ORGAN: PYLORIC CAECA KEYWDS PSYCHROPHILIC ENZYMES, PROTEINASE-CATALYZED PEPTIDE COUPLING, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.TOYOTA,K.K.S.NG,S.KUNINAGA,H.SEKIZAKI,K.ITOH,K.TANIZAWA,M.N.G.JAMES REVDAT 3 30-OCT-24 1MBQ 1 REMARK LINK REVDAT 2 24-FEB-09 1MBQ 1 VERSN REVDAT 1 11-DEC-02 1MBQ 0 JRNL AUTH E.TOYOTA,K.K.S.NG,S.KUNINAGA,H.SEKIZAKI,K.ITOH,K.TANIZAWA, JRNL AUTH 2 M.N.G.JAMES JRNL TITL CRYSTAL STRUCTURE AND NUCLEOTIDE SEQUENCE OF AN ANIONIC JRNL TITL 2 TRYPSIN FROM CHUM SALMON (ONCORHYNCHUS KETA) IN COMPARISON JRNL TITL 3 WITH ATLANTIC SALMON (SALMO SALAR) AND BOVINE TRYPSIN JRNL REF J.MOL.BIOL. V. 324 391 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12445776 JRNL DOI 10.1016/S0022-2836(02)01097-5 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.80 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) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 17234 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) : 0.166 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1708 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 : 1647 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 91 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) : 0.57200 REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : -0.11400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : 0.00000 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) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.290 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) : 1.024 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.991 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.518 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.854 ; 2.500 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : BEN.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : BEN.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016804. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 8.15 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DOUBLE-FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE DIP100 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17253 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.310 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06700 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.25 REMARK 200 R MERGE FOR SHELL (I) : 0.18300 REMARK 200 R SYM FOR SHELL (I) : 0.18300 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2TBS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM SULFATE, TRIS, CALCIUM REMARK 280 CHLORIDE, TRIS-CL, BENZAMIDINE, PH 8.15, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 22.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.48000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.00500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.48000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.00500 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 HIS A 71 -59.81 -130.69 REMARK 500 ASN A 115 -158.37 -156.87 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 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE1 REMARK 620 2 ASN A 72 O 90.5 REMARK 620 3 VAL A 75 O 165.9 83.6 REMARK 620 4 GLU A 77 OE1 94.9 86.2 97.5 REMARK 620 5 GLU A 80 OE2 99.1 169.0 88.2 87.7 REMARK 620 6 HOH A1248 O 82.2 97.9 86.0 174.9 88.7 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 1222 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2TBS RELATED DB: PDB REMARK 900 ANIONIC TRYPSIN FROM ATLANTIC SALMON DBREF 1MBQ A 16 243 UNP Q8AV11 Q8AV11_ONCKE 1 220 SEQRES 1 A 220 ILE VAL GLY GLY TYR GLU CYS LYS ALA TYR SER GLN PRO 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 ASN GLU ASN TRP VAL VAL SER ALA ALA SEQRES 4 A 220 HIS CYS TYR LYS SER ARG VAL GLU VAL ARG LEU GLY GLU SEQRES 5 A 220 HIS ASN ILE LYS VAL THR GLU GLY SER GLU GLN PHE ILE SEQRES 6 A 220 SER SER SER ARG VAL ILE ARG HIS PRO ASN TYR SER SER SEQRES 7 A 220 TYR ASN ILE ASP ASN ASP ILE MET LEU ILE LYS LEU SER SEQRES 8 A 220 LYS SER ALA THR LEU ASN THR TYR VAL GLN PRO VAL ALA SEQRES 9 A 220 LEU PRO SER SER CYS ALA PRO ALA GLY THR MET CYS THR SEQRES 10 A 220 VAL SER GLY TRP GLY ASN THR MET SER SER THR ALA ASP SEQRES 11 A 220 LYS ASN LYS LEU GLN CYS LEU ASN ILE PRO ILE LEU SER SEQRES 12 A 220 TYR SER ASP CYS ASN ASN SER TYR PRO GLY MET ILE THR SEQRES 13 A 220 ASN ALA 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 GLU LEU GLN GLY VAL VAL SER TRP GLY TYR GLY SEQRES 16 A 220 CYS ALA GLU PRO GLY ASN PRO GLY VAL TYR ALA LYS VAL SEQRES 17 A 220 CYS ILE PHE ASN ASP TRP LEU THR SER THR MET ALA HET CA A 1 1 HET BEN A1222 9 HETNAM CA CALCIUM ION HETNAM BEN BENZAMIDINE FORMUL 2 CA CA 2+ FORMUL 3 BEN C7 H8 N2 FORMUL 4 HOH *91(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 PHE A 234 MET A 242 1 9 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 VAL A 138 O LEU A 158 SHEET 4 A 7 PRO A 198 CYS A 201 -1 O VAL A 200 N THR A 137 SHEET 5 A 7 GLU A 204 TRP A 215 -1 O GLU 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 GLU A 64 LEU A 67 -1 N VAL A 65 O ILE A 83 SHEET 7 B 7 GLN A 30 ASN A 34 -1 N ASN A 34 O GLU 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 LINK CA CA A 1 OE1 GLU A 70 1555 1555 2.18 LINK CA CA A 1 O ASN A 72 1555 1555 2.36 LINK CA CA A 1 O VAL A 75 1555 1555 2.23 LINK CA CA A 1 OE1 GLU A 77 1555 1555 2.35 LINK CA CA A 1 OE2 GLU A 80 1555 1555 2.23 LINK CA CA A 1 O HOH A1248 1555 1555 2.32 SITE 1 AC1 6 GLU A 70 ASN A 72 VAL A 75 GLU A 77 SITE 2 AC1 6 GLU A 80 HOH A1248 SITE 1 AC2 8 ASP A 189 SER A 190 CYS A 191 SER A 195 SITE 2 AC2 8 GLY A 216 GLY A 219 GLY A 226 HOH A1237 CRYST1 44.930 48.010 82.960 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 0.022257 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012054 0.00000