HEADER HYDROLASE ZYMOGEN (SERINE PROTEINASE) 17-MAR-86 2TGD TITLE LACK OF THE TRANSITION STATE STABILIZATION SITE IS A FACTOR IN THE TITLE 2 INACTIVITY OF TRYPSINOGEN, A SERINE PROTEASE ZYMOGEN. STRUCTURE OF TITLE 3 DFP INHIBITED BOVINE TRYPSINOGEN AT 2.1 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSINOGEN; 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 HYDROLASE ZYMOGEN (SERINE PROTEINASE) EXPDTA X-RAY DIFFRACTION AUTHOR M.O.JONES,R.M.STROUD REVDAT 3 29-NOV-17 2TGD 1 HELIX REVDAT 2 24-FEB-09 2TGD 1 VERSN REVDAT 1 07-MAY-86 2TGD 0 JRNL AUTH M.O.JONES,R.M.STROUD JRNL TITL LACK OF THE TRANSITION STATE STABILIZATION SITE IS A FACTOR JRNL TITL 2 IN THE INACTIVITY OF TRYPSINOGEN, A SERINE PROTEASE ZYMOGEN. JRNL TITL 3 STRUCTURE OF DFP INHIBITED BOVINE TRYPSINOGEN AT 2.1 JRNL TITL 4 ANGSTROMS RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.A.KOSSIAKOFF,J.L.CHAMBERS,L.M.KAY,R.M.STROUD REMARK 1 TITL STRUCTURE OF BOVINE TRYPSINOGEN AT 1.9 ANGSTROMS RESOLUTION REMARK 1 REF BIOCHEMISTRY V. 16 654 1977 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.M.STROUD,A.A.KOSSIAKOFF,J.L.CHAMBERS REMARK 1 TITL MECHANISMS OF ZYMOGEN ACTIVATION REMARK 1 REF ANNU.REV.BIOPHYS.BIOENG. V. 6 177 1977 REMARK 1 REFN ISSN 0084-6589 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL 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) : 0.182 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 : 1616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 73 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) : 0.025 REMARK 3 BOND ANGLES (DEGREES) : 3.050 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 5.490 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 2TGD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178672. 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 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 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 (%): 38.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.43333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.86667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.86667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.43333 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 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 VAL A 10 REMARK 465 ASP A 11 REMARK 465 ASP A 12 REMARK 465 ASP A 13 REMARK 465 ASP A 14 REMARK 465 LYS A 15 REMARK 465 ILE A 16 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 188A CB CG CD CE NZ 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 247 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 72 O REMARK 620 2 VAL A 75 O 74.4 REMARK 620 3 GLU A 80 OE2 160.2 91.4 REMARK 620 4 HOH A 263 O 89.4 102.3 80.0 REMARK 620 5 GLU A 70 OE1 96.1 159.6 101.5 95.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: BIN REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: SPECIFIC BINDING POCKET REMARK 800 REMARK 800 SITE_IDENTIFIER: ION REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CALCIUM ION BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DFP A 248 DBREF 2TGD A 10 245 UNP P00760 TRY1_BOVIN 15 243 SEQRES 1 A 229 VAL ASP ASP ASP ASP LYS ILE VAL GLY GLY TYR THR CYS SEQRES 2 A 229 GLY ALA ASN THR VAL PRO TYR GLN VAL SER LEU ASN SER SEQRES 3 A 229 GLY TYR HIS PHE CYS GLY GLY SER LEU ILE ASN SER GLN SEQRES 4 A 229 TRP VAL VAL SER ALA ALA HIS CYS TYR LYS SER GLY ILE SEQRES 5 A 229 GLN VAL ARG LEU GLY GLU ASP ASN ILE ASN VAL VAL GLU SEQRES 6 A 229 GLY ASN GLU GLN PHE ILE SER ALA SER LYS SER ILE VAL SEQRES 7 A 229 HIS PRO SER TYR ASN SER ASN THR LEU ASN ASN ASP ILE SEQRES 8 A 229 MET LEU ILE LYS LEU LYS SER ALA ALA SER LEU ASN SER SEQRES 9 A 229 ARG VAL ALA SER ILE SER LEU PRO THR SER CYS ALA SER SEQRES 10 A 229 ALA GLY THR GLN CYS LEU ILE SER GLY TRP GLY ASN THR SEQRES 11 A 229 LYS SER SER GLY THR SER TYR PRO ASP VAL LEU LYS CYS SEQRES 12 A 229 LEU LYS ALA PRO ILE LEU SER ASP SER SER CYS LYS SER SEQRES 13 A 229 ALA TYR PRO GLY GLN ILE THR SER ASN MET PHE CYS ALA SEQRES 14 A 229 GLY TYR LEU GLU GLY GLY LYS ASP SER CYS GLN GLY ASP SEQRES 15 A 229 SER GLY GLY PRO VAL VAL CYS SER GLY LYS LEU GLN GLY SEQRES 16 A 229 ILE VAL SER TRP GLY SER GLY CYS ALA GLN LYS ASN LYS SEQRES 17 A 229 PRO GLY VAL TYR THR LYS VAL CYS ASN TYR VAL SER TRP SEQRES 18 A 229 ILE LYS GLN THR ILE ALA SER ASN HET CA A 247 1 HET DFP A 248 10 HETNAM CA CALCIUM ION HETNAM DFP DIISOPROPYL PHOSPHONATE FORMUL 2 CA CA 2+ FORMUL 3 DFP C6 H15 O3 P FORMUL 4 HOH *73(H2 O) HELIX 1 SHO SER A 164 TYR A 172 1IRREGULAR AFTER CYS 168 9 HELIX 2 310 LYS A 230 VAL A 235 5LEADS INTO TERMINAL ALPHA-HLX 6 HELIX 3 TER TYR A 234 ASN A 245 1C-TERMINAL HELIX 12 SHEET 1 SH1 7 TYR A 20 TYR A 20 0 SHEET 2 SH1 7 LYS A 156 PRO A 161 -1 N TYR A 20 O CYS A 157 SHEET 3 SH1 7 CYS A 136 GLY A 140 -1 N LEU A 158 O ILE A 138 SHEET 4 SH1 7 GLY A 197 CYS A 201 -1 N VAL A 200 O LEU A 137 SHEET 5 SH1 7 LYS A 204 SER A 214 -1 N VAL A 213 O GLY A 197 SHEET 6 SH1 7 GLY A 226 VAL A 231 -1 N THR A 229 O ILE A 212 SHEET 7 SH1 7 ASN A 179 ALA A 183 -1 N PHE A 181 O TYR A 228 SHEET 1 SH2 4 GLY A 43 SER A 45 0 SHEET 2 SH2 4 VAL A 52 ALA A 55 -1 N VAL A 53 O SER A 45 SHEET 3 SH2 4 MET A 104 LYS A 107 -1 N SER A 54 O MET A 104 SHEET 4 SH2 4 LYS A 87 HIS A 91 -1 N HIS A 91 O ILE A 103 SHEET 1 SH3 2 ILE A 63 LEU A 66 0 SHEET 2 SH3 2 GLN A 81 ALA A 85 -1 N GLN A 81 O LEU A 66 SSBOND 1 CYS A 22 CYS A 157 1555 1555 1.94 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.06 SSBOND 3 CYS A 128 CYS A 232 1555 1555 1.85 SSBOND 4 CYS A 136 CYS A 201 1555 1555 1.90 SSBOND 5 CYS A 168 CYS A 182 1555 1555 1.78 SSBOND 6 CYS A 191 CYS A 220 1555 1555 1.92 LINK OG SER A 195 P DFP A 248 1555 1555 1.54 LINK CA CA A 247 O ASN A 72 1555 1555 2.49 LINK CA CA A 247 O VAL A 75 1555 1555 2.21 LINK CA CA A 247 OE2 GLU A 80 1555 1555 2.45 LINK CA CA A 247 O HOH A 263 1555 1555 2.53 LINK CA CA A 247 OE1 GLU A 70 1555 1555 2.37 SITE 1 ACT 3 HIS A 57 ASP A 102 SER A 195 SITE 1 BIN 12 ASP A 189 SER A 190 CYS A 191 GLN A 192 SITE 2 BIN 12 GLY A 193 ASP A 194 SER A 214 TRP A 215 SITE 3 BIN 12 GLY A 216 SER A 217 GLY A 219 CYS A 220 SITE 1 ION 11 GLU A 70 ASP A 71 ASN A 72 ILE A 73 SITE 2 ION 11 ASN A 74 VAL A 75 VAL A 76 GLU A 77 SITE 3 ION 11 GLY A 78 ASN A 79 GLU A 80 SITE 1 AC1 6 GLU A 70 ASN A 72 VAL A 75 GLU A 77 SITE 2 AC1 6 GLU A 80 HOH A 263 SITE 1 AC2 7 PHE A 41 HIS A 57 GLY A 193 ASP A 194 SITE 2 AC2 7 SER A 195 HOH A 254 HOH A 257 CRYST1 55.150 55.150 109.300 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.577350 0.000000 0.00000 ORIGX2 0.000000 1.154701 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018132 0.010469 0.000000 0.00000 SCALE2 0.000000 0.020937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009149 0.00000