HEADER HYDROLASE 24-MAR-15 4YYR TITLE FICIN B CRYSTAL FORM I COMPND MOL_ID: 1; COMPND 2 MOLECULE: FICIN B; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FICUS CARICA; SOURCE 3 ORGANISM_TAXID: 3494 KEYWDS CYSTEINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.AZARKAN,D.BAEYENS-VOLANT,R.LORIS REVDAT 2 10-JAN-24 4YYR 1 REMARK REVDAT 1 13-APR-16 4YYR 0 JRNL AUTH F.BALDACCI-CRESP,J.A.RODRIGUEZ BUITRAGO,N.M'RABET,R.LORIS, JRNL AUTH 2 N.BAUCHER,D.BAEYENS-VOLANT,M.AZARKAN JRNL TITL CRYSTAL STRUCTURE OF FOUR VARIANTS OF THE PROTEASE FICIN JRNL TITL 2 FROM THE COMMON FIG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 53284 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2704 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 26.0541 - 2.9059 0.99 5613 295 0.1545 0.1600 REMARK 3 2 2.9059 - 2.3069 0.99 5496 272 0.1494 0.1595 REMARK 3 3 2.3069 - 2.0155 0.99 5432 296 0.1237 0.1410 REMARK 3 4 2.0155 - 1.8312 0.98 5344 297 0.1188 0.1535 REMARK 3 5 1.8312 - 1.7000 0.97 5289 293 0.1093 0.1417 REMARK 3 6 1.7000 - 1.5998 0.97 5236 278 0.0955 0.1319 REMARK 3 7 1.5998 - 1.5197 0.95 5153 300 0.0961 0.1405 REMARK 3 8 1.5197 - 1.4535 0.94 5125 257 0.1016 0.1534 REMARK 3 9 1.4535 - 1.3976 0.82 4472 227 0.1219 0.1603 REMARK 3 10 1.3976 - 1.3494 0.63 3420 189 0.1336 0.1781 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 40.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.500 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) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 1776 REMARK 3 ANGLE : 1.322 2426 REMARK 3 CHIRALITY : 0.084 269 REMARK 3 PLANARITY : 0.006 314 REMARK 3 DIHEDRAL : 12.452 646 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 4YYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53284 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.349 REMARK 200 RESOLUTION RANGE LOW (A) : 26.049 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4YYQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AS, 0.1 M NA HEPES 7.5, 2% REMARK 280 PEG400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 37.33067 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 18.66533 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 18.66533 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 37.33067 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: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 ARG A 21 CZ NH1 NH2 REMARK 470 VAL A 32 CG1 CG2 REMARK 470 LYS A 79 CD CE NZ REMARK 470 LYS A 148 CD CE NZ REMARK 470 ASP A 174 CG OD1 OD2 REMARK 470 ALA A 222 CA C O CB 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 161 -11.08 -144.80 REMARK 500 GLN A 212 72.93 -155.50 REMARK 500 SER A 221 -139.99 -94.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 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 Ligand residues SCH A 25 REMARK 800 through TRP A 26 bound to SER A 24 DBREF 4YYR A 1 222 PDB 4YYR 4YYR 1 222 SEQRES 1 A 222 LEU PRO GLU THR VAL ASP TRP ARG ILE GLN GLY ALA VAL SEQRES 2 A 222 ASN PRO ILE ARG ASN GLN GLY ARG CYS GLY SER SCH TRP SEQRES 3 A 222 ALA PHE SER VAL VAL VAL VAL VAL GLU GLY ILE THR LYS SEQRES 4 A 222 ILE VAL THR ASP GLU LEU PRO SER LEU SER GLU GLN GLN SEQRES 5 A 222 LEU VAL ASP CYS ALA THR SER TYR LYS ASN LEU GLY CYS SEQRES 6 A 222 SER GLY GLY TRP MET THR LYS ALA TYR ASP TYR ILE ILE SEQRES 7 A 222 LYS ASN GLY GLY ILE THR SER GLN SER ASN TYR PRO TYR SEQRES 8 A 222 THR ALA LYS LYS GLY GLU CYS ASN LYS ASP LEU ALA SER SEQRES 9 A 222 GLN ILE VAL ALA THR ILE ASP SER TYR GLU HIS VAL PRO SEQRES 10 A 222 ARG ASN ASN GLU ASN ALA LEU LYS ASN ALA VAL ALA ASN SEQRES 11 A 222 GLN PRO VAL SER VAL THR ILE GLU ALA GLY GLY ARG ALA SEQRES 12 A 222 PHE GLU LEU TYR LYS SER GLY VAL PHE VAL GLY SER CYS SEQRES 13 A 222 GLY THR LYS LEU ASP HIS ALA VAL VAL ALA ILE GLY TYR SEQRES 14 A 222 GLY SER GLU ASN ASP VAL ASP TYR TRP LEU VAL ARG ASN SEQRES 15 A 222 SER TRP GLY THR ASN TRP GLY GLU ARG GLY TYR ILE LYS SEQRES 16 A 222 LEU GLN ARG ASN VAL ALA GLU PRO THR GLY LYS CYS GLY SEQRES 17 A 222 ILE ALA MET GLN SER THR TYR PRO VAL LYS LYS THR SER SEQRES 18 A 222 ALA HET SCH A 25 8 HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SCH S-METHYL-THIO-CYSTEINE HETNAM SO4 SULFATE ION FORMUL 1 SCH C4 H9 N O2 S2 FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *359(H2 O) HELIX 1 AA1 SER A 24 ASP A 43 1 20 HELIX 2 AA2 SER A 49 ALA A 57 1 9 HELIX 3 AA3 SER A 59 LEU A 63 5 5 HELIX 4 AA4 TRP A 69 GLY A 81 1 13 HELIX 5 AA5 ASN A 99 SER A 104 1 6 HELIX 6 AA6 ASN A 120 GLN A 131 1 12 HELIX 7 AA7 GLY A 141 LEU A 146 1 6 HELIX 8 AA8 GLY A 205 ILE A 209 5 5 SHEET 1 AA1 3 VAL A 5 ASP A 6 0 SHEET 2 AA1 3 HIS A 162 GLU A 172 -1 O TYR A 169 N VAL A 5 SHEET 3 AA1 3 VAL A 133 ILE A 137 -1 N VAL A 133 O ALA A 166 SHEET 1 AA2 5 VAL A 5 ASP A 6 0 SHEET 2 AA2 5 HIS A 162 GLU A 172 -1 O TYR A 169 N VAL A 5 SHEET 3 AA2 5 VAL A 175 ARG A 181 -1 O ARG A 181 N VAL A 165 SHEET 4 AA2 5 TYR A 193 GLN A 197 -1 O LEU A 196 N TRP A 178 SHEET 5 AA2 5 VAL A 151 PHE A 152 1 N PHE A 152 O LYS A 195 SHEET 1 AA3 2 SER A 112 HIS A 115 0 SHEET 2 AA3 2 THR A 214 VAL A 217 -1 O TYR A 215 N GLU A 114 SSBOND 1 CYS A 22 CYS A 65 1555 1555 2.06 SSBOND 2 CYS A 56 CYS A 98 1555 1555 2.06 SSBOND 3 CYS A 156 CYS A 207 1555 1555 2.04 LINK C SER A 24 N SCH A 25 1555 1555 1.33 LINK C SCH A 25 N TRP A 26 1555 1555 1.33 SITE 1 AC1 9 LEU A 1 LYS A 72 GLU A 114 HIS A 115 SITE 2 AC1 9 HOH A 431 HOH A 456 HOH A 520 HOH A 550 SITE 3 AC1 9 HOH A 578 SITE 1 AC2 5 ARG A 21 ALA A 93 HOH A 401 HOH A 458 SITE 2 AC2 5 HOH A 471 SITE 1 AC3 20 GLN A 19 GLY A 23 SER A 24 ALA A 27 SITE 2 AC3 20 PHE A 28 SER A 29 VAL A 30 LEU A 53 SITE 3 AC3 20 GLY A 64 GLY A 67 GLY A 68 MET A 70 SITE 4 AC3 20 HIS A 162 ALA A 163 VAL A 164 ASN A 182 SITE 5 AC3 20 SER A 183 TRP A 184 SER A 221 ALA A 222 CRYST1 89.902 89.902 55.996 90.00 90.00 120.00 P 32 2 1 6 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 0.011123 0.006422 0.000000 0.00000 SCALE2 0.000000 0.012844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017858 0.00000