HEADER HYDROLASE 30-MAR-20 7BS2 TITLE BOVINE PANCREATIC TRYPSIN WITH SEROTONIN (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: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS MICROFLUIDIC DEVICE, CRYSTAL SORTING, ROOM TEMPERATURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.MAEKI,S.ITO,R.TAKEDA,T.FUNAKUBO,G.UENO,A.ISHIDA,H.TANI,M.YAMAMOTO, AUTHOR 2 M.TOKESHI REVDAT 3 29-NOV-23 7BS2 1 REMARK REVDAT 2 23-JUN-21 7BS2 1 JRNL REVDAT 1 26-AUG-20 7BS2 0 JRNL AUTH M.MAEKI,S.ITO,R.TAKEDA,G.UENO,A.ISHIDA,H.TANI,M.YAMAMOTO, JRNL AUTH 2 M.TOKESHI JRNL TITL ROOM-TEMPERATURE CRYSTALLOGRAPHY USING A MICROFLUIDIC JRNL TITL 2 PROTEIN CRYSTAL ARRAY DEVICE AND ITS APPLICATION TO JRNL TITL 3 PROTEIN-LIGAND COMPLEX STRUCTURE ANALYSIS. JRNL REF CHEM SCI V. 11 9072 2020 JRNL REFN ISSN 2041-6520 JRNL PMID 34094189 JRNL DOI 10.1039/D0SC02117B REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 19326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 945 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 44.2400 - 3.4400 0.87 2613 131 0.1117 0.1638 REMARK 3 2 3.4400 - 2.7300 0.94 2708 124 0.1477 0.1961 REMARK 3 3 2.7300 - 2.3900 0.95 2685 143 0.1516 0.1840 REMARK 3 4 2.3900 - 2.1700 0.94 2616 155 0.1515 0.2041 REMARK 3 5 2.1700 - 2.0100 0.94 2624 126 0.1546 0.2090 REMARK 3 6 2.0100 - 1.8900 0.93 2586 128 0.1778 0.1988 REMARK 3 7 1.8900 - 1.8000 0.91 2549 138 0.1998 0.2324 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.86 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7BS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-20. REMARK 100 THE DEPOSITION ID IS D_1300016388. 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) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32490 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 44.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : 3.683 REMARK 200 R MERGE (I) : 0.25500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.7100 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) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.66 REMARK 200 R MERGE FOR SHELL (I) : 2.03300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: 1S0Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 27.54500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.79000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.79000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.26000 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: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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: 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 76 -76.37 -118.83 REMARK 500 SER A 215 -63.58 -120.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 621 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 622 DISTANCE = 6.55 ANGSTROMS 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 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 75 OE1 REMARK 620 2 ASN A 77 O 89.6 REMARK 620 3 VAL A 80 O 162.4 82.7 REMARK 620 4 GLU A 85 OE2 103.2 162.0 88.2 REMARK 620 5 HOH A 403 O 89.7 90.2 106.0 77.4 REMARK 620 6 HOH A 505 O 79.2 103.2 87.1 91.7 162.4 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SRO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 DBREF 7BS2 A 24 246 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 CA A 301 1 HET SRO A 302 25 HET SO4 A 303 5 HETNAM CA CALCIUM ION HETNAM SRO SEROTONIN HETNAM SO4 SULFATE ION HETSYN SRO 3-(2-AMINOETHYL)-1H-INDOL-5-OL FORMUL 2 CA CA 2+ FORMUL 3 SRO C10 H12 N2 O FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *222(H2 O) HELIX 1 AA1 ALA A 61 TYR A 65 5 5 HELIX 2 AA2 SER A 167 TYR A 175 1 9 HELIX 3 AA3 TYR A 235 ASN A 246 1 12 SHEET 1 AA1 7 TYR A 28 THR A 29 0 SHEET 2 AA1 7 LYS A 159 PRO A 164 -1 O CYS A 160 N TYR A 28 SHEET 3 AA1 7 GLN A 138 GLY A 143 -1 N ILE A 141 O LEU A 161 SHEET 4 AA1 7 PRO A 203 CYS A 206 -1 O VAL A 205 N LEU A 140 SHEET 5 AA1 7 LYS A 209 TRP A 216 -1 O GLN A 211 N VAL A 204 SHEET 6 AA1 7 GLY A 227 LYS A 231 -1 O VAL A 228 N TRP A 216 SHEET 7 AA1 7 MET A 183 ALA A 186 -1 N PHE A 184 O TYR A 229 SHEET 1 AA2 7 GLN A 38 ASN A 42 0 SHEET 2 AA2 7 HIS A 46 ASN A 54 -1 O CYS A 48 N LEU A 41 SHEET 3 AA2 7 TRP A 57 SER A 60 -1 O VAL A 59 N SER A 51 SHEET 4 AA2 7 MET A 109 LEU A 113 -1 O ILE A 111 N VAL A 58 SHEET 5 AA2 7 GLN A 86 VAL A 95 -1 N SER A 91 O LYS A 112 SHEET 6 AA2 7 GLN A 70 LEU A 73 -1 N LEU A 73 O GLN A 86 SHEET 7 AA2 7 GLN A 38 ASN A 42 -1 N SER A 40 O ARG A 72 SSBOND 1 CYS A 30 CYS A 160 1555 1555 2.02 SSBOND 2 CYS A 48 CYS A 64 1555 1555 2.04 SSBOND 3 CYS A 132 CYS A 233 1555 1555 2.03 SSBOND 4 CYS A 139 CYS A 206 1555 1555 2.03 SSBOND 5 CYS A 171 CYS A 185 1555 1555 2.03 SSBOND 6 CYS A 196 CYS A 220 1555 1555 2.03 LINK OE1 GLU A 75 CA CA A 301 1555 1555 2.29 LINK O ASN A 77 CA CA A 301 1555 1555 2.27 LINK O VAL A 80 CA CA A 301 1555 1555 2.23 LINK OE2 GLU A 85 CA CA A 301 1555 1555 2.37 LINK CA CA A 301 O HOH A 403 1555 1555 2.32 LINK CA CA A 301 O HOH A 505 1555 1555 2.43 SITE 1 AC1 6 GLU A 75 ASN A 77 VAL A 80 GLU A 85 SITE 2 AC1 6 HOH A 403 HOH A 505 SITE 1 AC2 11 ASP A 194 SER A 195 CYS A 196 GLN A 197 SITE 2 AC2 11 SER A 200 SER A 207 SER A 215 TRP A 216 SITE 3 AC2 11 GLY A 217 HOH A 489 HOH A 579 SITE 1 AC3 6 PRO A 129 THR A 130 SER A 131 GLY A 151 SITE 2 AC3 6 LYS A 209 GLN A 211 CRYST1 55.090 58.520 67.580 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 0.018152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014797 0.00000