HEADER HYDROLASE 30-JAN-20 6XYK TITLE CRYSTAL STRUCTURE OF BOVINE TRYPSIN AT ROOM TEMPERATURE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATIONIC TRYPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-TRYPSIN; COMPND 5 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 SERINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.JENSEN REVDAT 3 24-JAN-24 6XYK 1 REMARK REVDAT 2 04-AUG-21 6XYK 1 COMPND REMARK HET FORMUL REVDAT 2 2 1 SITE ATOM REVDAT 1 27-JAN-21 6XYK 0 JRNL AUTH M.JENSEN JRNL TITL FEMTOSECOND STRUCTURE OF BOVINE TRYPSIN AT ROOM TEMPERATURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.383 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35417 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.998 REMARK 3 FREE R VALUE TEST SET COUNT : 1770 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.2900 - 3.5251 1.00 2773 146 0.1314 0.1218 REMARK 3 2 3.5251 - 2.7987 1.00 2634 138 0.1504 0.1877 REMARK 3 3 2.7987 - 2.4451 1.00 2609 138 0.1596 0.1543 REMARK 3 4 2.4451 - 2.2216 1.00 2603 136 0.1494 0.1818 REMARK 3 5 2.2216 - 2.0625 1.00 2593 137 0.1407 0.1769 REMARK 3 6 2.0625 - 1.9409 1.00 2559 135 0.1379 0.1668 REMARK 3 7 1.9409 - 1.8437 1.00 2581 136 0.1418 0.1791 REMARK 3 8 1.8437 - 1.7635 1.00 2563 134 0.1453 0.1713 REMARK 3 9 1.7635 - 1.6956 1.00 2568 136 0.1426 0.1684 REMARK 3 10 1.6956 - 1.6371 1.00 2530 133 0.1390 0.1559 REMARK 3 11 1.6371 - 1.5859 1.00 2565 135 0.1413 0.1579 REMARK 3 12 1.5859 - 1.5406 1.00 2538 133 0.1475 0.1983 REMARK 3 13 1.5406 - 1.5000 1.00 2531 133 0.1647 0.1999 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.107 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.874 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.55 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1679 REMARK 3 ANGLE : 0.800 2281 REMARK 3 CHIRALITY : 0.060 254 REMARK 3 PLANARITY : 0.005 291 REMARK 3 DIHEDRAL : 4.131 983 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35707 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4100 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) : 1.54 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4IH8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG8000, 50 MM HEPES PH 7.0, 0.2 M REMARK 280 AMMONIUM SULFATE, 3 MM CACL2AND 6 MG/ML BENZAMIDINE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 27.41500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.70500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.70500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.29000 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 TOTAL BURIED SURFACE AREA: 690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 146 OE1 GLN A 189 2.15 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 68 -77.23 -116.42 REMARK 500 SER A 207 -64.41 -121.65 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 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 67 OE1 REMARK 620 2 ASN A 69 O 90.6 REMARK 620 3 VAL A 72 O 165.1 81.4 REMARK 620 4 GLU A 77 OE2 102.2 160.2 89.0 REMARK 620 5 HOH A 407 O 87.5 87.8 104.7 77.9 REMARK 620 6 HOH A 511 O 80.5 102.7 88.8 94.3 164.1 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 BEN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XYG RELATED DB: PDB DBREF 6XYK A 16 238 UNP P00760 TRY1_BOVIN 24 246 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 BEN A 301 9 HET SO4 A 302 5 HET CA A 303 1 HETNAM BEN BENZAMIDINE HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION FORMUL 2 BEN C7 H8 N2 FORMUL 3 SO4 O4 S 2- FORMUL 4 CA CA 2+ FORMUL 5 HOH *219(H2 O) HELIX 1 AA1 ALA A 53 TYR A 57 5 5 HELIX 2 AA2 SER A 159 TYR A 167 1 9 HELIX 3 AA3 TYR A 227 SER A 237 1 11 SHEET 1 AA1 7 TYR A 20 THR A 21 0 SHEET 2 AA1 7 LYS A 151 PRO A 156 -1 O CYS A 152 N TYR A 20 SHEET 3 AA1 7 GLN A 130 GLY A 135 -1 N ILE A 133 O LEU A 153 SHEET 4 AA1 7 PRO A 195 CYS A 198 -1 O VAL A 197 N LEU A 132 SHEET 5 AA1 7 LYS A 201 TRP A 208 -1 O LYS A 201 N CYS A 198 SHEET 6 AA1 7 GLY A 219 LYS A 223 -1 O VAL A 220 N TRP A 208 SHEET 7 AA1 7 MET A 175 ALA A 178 -1 N PHE A 176 O TYR A 221 SHEET 1 AA2 7 GLN A 30 ASN A 34 0 SHEET 2 AA2 7 HIS A 38 ASN A 46 -1 O CYS A 40 N LEU A 33 SHEET 3 AA2 7 TRP A 49 SER A 52 -1 O VAL A 51 N SER A 43 SHEET 4 AA2 7 MET A 101 LEU A 105 -1 O ILE A 103 N VAL A 50 SHEET 5 AA2 7 GLN A 78 VAL A 87 -1 N ILE A 86 O LEU A 102 SHEET 6 AA2 7 GLN A 62 LEU A 65 -1 N LEU A 65 O GLN A 78 SHEET 7 AA2 7 GLN A 30 ASN A 34 -1 N SER A 32 O ARG A 64 SSBOND 1 CYS A 22 CYS A 152 1555 1555 2.04 SSBOND 2 CYS A 40 CYS A 56 1555 1555 2.03 SSBOND 3 CYS A 124 CYS A 225 1555 1555 2.02 SSBOND 4 CYS A 131 CYS A 198 1555 1555 2.03 SSBOND 5 CYS A 163 CYS A 177 1555 1555 2.03 SSBOND 6 CYS A 188 CYS A 212 1555 1555 2.03 LINK OE1 GLU A 67 CA CA A 303 1555 1555 2.27 LINK O ASN A 69 CA CA A 303 1555 1555 2.31 LINK O VAL A 72 CA CA A 303 1555 1555 2.25 LINK OE2 GLU A 77 CA CA A 303 1555 1555 2.32 LINK CA CA A 303 O HOH A 407 1555 1555 2.40 LINK CA CA A 303 O HOH A 511 1555 1555 2.38 SITE 1 AC1 8 ASP A 186 SER A 187 SER A 192 GLY A 209 SITE 2 AC1 8 GLY A 211 GLY A 219 SO4 A 302 HOH A 521 SITE 1 AC2 6 HIS A 55 GLN A 189 GLY A 190 SER A 192 SITE 2 AC2 6 BEN A 301 HOH A 497 SITE 1 AC3 6 GLU A 67 ASN A 69 VAL A 72 GLU A 77 SITE 2 AC3 6 HOH A 407 HOH A 511 CRYST1 54.830 58.580 67.410 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 0.018238 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017071 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014835 0.00000