PDB Short entry for 2ZPS HEADER HYDROLASE 28-JUL-08 2ZPS TITLE CRYSTAL STRUCTURE OF ANIONIC TRYPSIN ISOFORM 3 FROM CHUM SALMON COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANIONIC TRYPSIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ONCORHYNCHUS KETA; SOURCE 3 ORGANISM_COMMON: CHUM SALMON; SOURCE 4 ORGANISM_TAXID: 8018 KEYWDS SERINE PROTEINASE, TRYPSIN, HYDROLASE, PROTEASE, SERINE PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR D.IYAGUCHI,E.TOYOTA REVDAT 2 28-SEP-16 2ZPS 1 REMARK VERSN REVDAT 1 28-JUL-09 2ZPS 0 JRNL AUTH E.TOYOTA,D.IYAGUCHI,H.SEKIZAKI,M.TATEYAMA,K.K.NG JRNL TITL A STRUCTURAL COMPARISON OF THREE ISOFORMS OF ANIONIC TRYPSIN JRNL TITL 2 FROM CHUM SALMON (ONCORHYNCHUS KETA). JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 717 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19564692 JRNL DOI 10.1107/S0907444909012165 REMARK 2 REMARK 2 RESOLUTION. 1.55 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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 : 27350 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) : 0.186 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2742 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 : 1655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 233 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 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 2ZPS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB028272. 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 : 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 MICROMAX-007 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 : 27417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04000 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) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.12200 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 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 22.18550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.75400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.76550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.75400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.18550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.76550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 TYR A 222 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 53 -66.02 -128.18 REMARK 500 ASN A 80 -5.04 -140.58 REMARK 500 SER A 191 -64.78 -121.63 REMARK 500 ASN A 201 76.26 -119.39 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 A2001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 ASN A 54 O 91.3 REMARK 620 3 VAL A 57 O 163.0 81.9 REMARK 620 4 GLU A 59 OE1 96.8 84.2 98.0 REMARK 620 5 GLU A 62 OE2 101.0 163.0 89.2 82.7 REMARK 620 6 HOH A2018 O 78.2 105.7 88.6 168.8 88.4 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 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZPQ RELATED DB: PDB REMARK 900 ISOFORM 1 REMARK 900 RELATED ID: 2ZPR RELATED DB: PDB REMARK 900 ISOFORM 2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 ISOFORM AT THESE POSITIONS DBREF 2ZPS A 1 222 UNP Q8AV11 Q8AV11_ONCKE 1 222 SEQADV 2ZPS THR A 44 UNP Q8AV11 SER 44 SEE REMARK 999 SEQADV 2ZPS ASN A 213 UNP Q8AV11 ASP 213 SEE REMARK 999 SEQRES 1 A 222 ILE VAL GLY GLY TYR GLU CYS LYS ALA TYR SER GLN PRO SEQRES 2 A 222 HIS GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 A 222 GLY SER LEU VAL ASN GLU ASN TRP VAL VAL SER ALA ALA SEQRES 4 A 222 HIS CYS TYR LYS THR ARG VAL GLU VAL ARG LEU GLY GLU SEQRES 5 A 222 HIS ASN ILE LYS VAL THR GLU GLY SER GLU GLN PHE ILE SEQRES 6 A 222 SER SER SER ARG VAL ILE ARG HIS PRO ASN TYR SER SER SEQRES 7 A 222 TYR ASN ILE ASP ASN ASP ILE MET LEU ILE LYS LEU SER SEQRES 8 A 222 LYS PRO ALA THR LEU ASN THR TYR VAL GLN PRO VAL ALA SEQRES 9 A 222 LEU PRO SER SER CYS ALA PRO ALA GLY THR MET CYS THR SEQRES 10 A 222 VAL SER GLY TRP GLY ASN THR MET SER SER THR ALA ASP SEQRES 11 A 222 LYS ASN LYS LEU GLN CYS LEU ASN ILE PRO ILE LEU SER SEQRES 12 A 222 TYR SER ASP CYS ASN ASN SER TYR PRO GLY MET ILE THR SEQRES 13 A 222 ASN ALA MET PHE CYS ALA GLY TYR LEU GLU GLY GLY LYS SEQRES 14 A 222 ASP SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL CYS SEQRES 15 A 222 ASN GLY GLU LEU GLN GLY VAL VAL SER TRP GLY TYR GLY SEQRES 16 A 222 CYS ALA GLU PRO GLY ASN PRO GLY VAL TYR ALA LYS VAL SEQRES 17 A 222 CYS ILE PHE ASN ASN TRP LEU THR SER THR MET ALA THR SEQRES 18 A 222 TYR HET CA A2001 1 HET BEN A1001 9 HETNAM CA CALCIUM ION HETNAM BEN BENZAMIDINE FORMUL 2 CA CA 2+ FORMUL 3 BEN C7 H8 N2 FORMUL 4 HOH *233(H2 O) HELIX 1 1 ALA A 38 TYR A 42 5 5 HELIX 2 2 SER A 143 TYR A 151 1 9 HELIX 3 3 PHE A 211 MET A 219 1 9 SHEET 1 A 7 TYR A 5 GLU A 6 0 SHEET 2 A 7 GLN A 135 PRO A 140 -1 O CYS A 136 N TYR A 5 SHEET 3 A 7 MET A 115 GLY A 120 -1 N VAL A 118 O LEU A 137 SHEET 4 A 7 PRO A 179 CYS A 182 -1 O VAL A 181 N THR A 117 SHEET 5 A 7 GLU A 185 TRP A 192 -1 O GLU A 185 N CYS A 182 SHEET 6 A 7 GLY A 203 LYS A 207 -1 O VAL A 204 N TRP A 192 SHEET 7 A 7 MET A 159 ALA A 162 -1 N PHE A 160 O TYR A 205 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 ILE A 88 N VAL A 35 SHEET 5 B 7 GLN A 63 ARG A 72 -1 N ILE A 71 O LEU A 87 SHEET 6 B 7 GLU A 47 LEU A 50 -1 N VAL A 48 O ILE A 65 SHEET 7 B 7 GLN A 15 ASN A 19 -1 N ASN A 19 O GLU A 47 SSBOND 1 CYS A 7 CYS A 136 1555 1555 2.03 SSBOND 2 CYS A 25 CYS A 41 1555 1555 2.03 SSBOND 3 CYS A 109 CYS A 209 1555 1555 2.03 SSBOND 4 CYS A 116 CYS A 182 1555 1555 2.03 SSBOND 5 CYS A 147 CYS A 161 1555 1555 2.03 SSBOND 6 CYS A 172 CYS A 196 1555 1555 2.03 LINK OE1 GLU A 52 CA CA A2001 1555 1555 2.23 LINK O ASN A 54 CA CA A2001 1555 1555 2.29 LINK O VAL A 57 CA CA A2001 1555 1555 2.24 LINK OE1 GLU A 59 CA CA A2001 1555 1555 2.46 LINK OE2 GLU A 62 CA CA A2001 1555 1555 2.29 LINK CA CA A2001 O HOH A2018 1555 1555 2.28 SITE 1 AC1 5 GLU A 52 ASN A 54 GLU A 59 GLU A 62 SITE 2 AC1 5 HOH A2018 SITE 1 AC2 8 ASP A 170 SER A 171 CYS A 172 SER A 176 SITE 2 AC2 8 GLY A 193 GLY A 195 GLY A 203 HOH A2016 CRYST1 44.371 47.531 81.508 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 0.022537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012269 0.00000