HEADER HYDROLASE 04-AUG-17 5QBH TITLE CRYSTAL STRUCTURE OF ENDOTHIAPEPSIN-FRG270 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOTHIAPEPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASPARTATE PROTEASE; COMPND 5 EC: 3.4.23.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRYPHONECTRIA PARASITICA; SOURCE 3 ORGANISM_COMMON: CHESTNUT BLIGHT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5116 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.HUSCHMANN REVDAT 2 17-NOV-21 5QBH 1 REMARK REVDAT 1 22-APR-20 5QBH 0 JRNL AUTH F.U.HUSCHMANN,M.S.WEISS,U.MUELLER,L.O.HAUSTEDT,G.KLEBE JRNL TITL CRYSTAL STRUCTURE OF ENDOTHIAPEPSIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 53364 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.870 REMARK 3 FREE R VALUE TEST SET COUNT : 998 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 42.7299 - 2.8091 1.00 7893 151 0.1342 0.1407 REMARK 3 2 2.8091 - 2.2297 1.00 7824 149 0.1315 0.1899 REMARK 3 3 2.2297 - 1.9478 1.00 7764 148 0.1043 0.1251 REMARK 3 4 1.9478 - 1.7697 1.00 7782 148 0.1145 0.1640 REMARK 3 5 1.7697 - 1.6429 1.00 7753 148 0.1338 0.2010 REMARK 3 6 1.6429 - 1.5460 0.97 7549 144 0.1645 0.2533 REMARK 3 7 1.5460 - 1.4686 0.75 5801 110 0.2076 0.2791 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.03 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 2586 REMARK 3 ANGLE : 0.997 3557 REMARK 3 CHIRALITY : 0.040 423 REMARK 3 PLANARITY : 0.004 460 REMARK 3 DIHEDRAL : 10.310 881 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 5QBH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1001401738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53365 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 42.712 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.790 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY 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 (%): 49.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE, 24-30% PEG 4000; CRYSTALS OBTAINED BY STREAK-SEEDING, REMARK 280 PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.61350 REMARK 290 SMTRY3 2 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 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 LYS A 191 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE A 300 CA CB CG1 CG2 CD1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D8M A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 405 DBREF 5QBH A 1 330 UNP P11838 CARP_CRYPA 90 419 SEQRES 1 A 330 SER THR GLY SER ALA THR THR THR PRO ILE ASP SER LEU SEQRES 2 A 330 ASP ASP ALA TYR ILE THR PRO VAL GLN ILE GLY THR PRO SEQRES 3 A 330 ALA GLN THR LEU ASN LEU ASP PHE ASP THR GLY SER SER SEQRES 4 A 330 ASP LEU TRP VAL PHE SER SER GLU THR THR ALA SER GLU SEQRES 5 A 330 VAL ASP GLY GLN THR ILE TYR THR PRO SER LYS SER THR SEQRES 6 A 330 THR ALA LYS LEU LEU SER GLY ALA THR TRP SER ILE SER SEQRES 7 A 330 TYR GLY ASP GLY SER SER SER SER GLY ASP VAL TYR THR SEQRES 8 A 330 ASP THR VAL SER VAL GLY GLY LEU THR VAL THR GLY GLN SEQRES 9 A 330 ALA VAL GLU SER ALA LYS LYS VAL SER SER SER PHE THR SEQRES 10 A 330 GLU ASP SER THR ILE ASP GLY LEU LEU GLY LEU ALA PHE SEQRES 11 A 330 SER THR LEU ASN THR VAL SER PRO THR GLN GLN LYS THR SEQRES 12 A 330 PHE PHE ASP ASN ALA LYS ALA SER LEU ASP SER PRO VAL SEQRES 13 A 330 PHE THR ALA ASP LEU GLY TYR HIS ALA PRO GLY THR TYR SEQRES 14 A 330 ASN PHE GLY PHE ILE ASP THR THR ALA TYR THR GLY SER SEQRES 15 A 330 ILE THR TYR THR ALA VAL SER THR LYS GLN GLY PHE TRP SEQRES 16 A 330 GLU TRP THR SER THR GLY TYR ALA VAL GLY SER GLY THR SEQRES 17 A 330 PHE LYS SER THR SER ILE ASP GLY ILE ALA ASP THR GLY SEQRES 18 A 330 THR THR LEU LEU TYR LEU PRO ALA THR VAL VAL SER ALA SEQRES 19 A 330 TYR TRP ALA GLN VAL SER GLY ALA LYS SER SER SER SER SEQRES 20 A 330 VAL GLY GLY TYR VAL PHE PRO CYS SER ALA THR LEU PRO SEQRES 21 A 330 SER PHE THR PHE GLY VAL GLY SER ALA ARG ILE VAL ILE SEQRES 22 A 330 PRO GLY ASP TYR ILE ASP PHE GLY PRO ILE SER THR GLY SEQRES 23 A 330 SER SER SER CYS PHE GLY GLY ILE GLN SER SER ALA GLY SEQRES 24 A 330 ILE GLY ILE ASN ILE PHE GLY ASP VAL ALA LEU LYS ALA SEQRES 25 A 330 ALA PHE VAL VAL PHE ASN GLY ALA THR THR PRO THR LEU SEQRES 26 A 330 GLY PHE ALA SER LYS HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HET D8M A 404 20 HET ACT A 405 4 HETNAM GOL GLYCEROL HETNAM D8M 2-[(2S,3R,4S,5R)-5-(AMINOMETHYL)-3,4- HETNAM 2 D8M DIHYDROXYTETRAHYDROFURAN-2-YL]-N-(PYRIDIN-2-YLMETHYL) HETNAM 3 D8M ACETAMIDE HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 D8M C13 H19 N3 O4 FORMUL 6 ACT C2 H3 O2 1- FORMUL 7 HOH *256(H2 O) HELIX 1 AA1 THR A 49 VAL A 53 5 5 HELIX 2 AA2 THR A 60 SER A 64 5 5 HELIX 3 AA3 SER A 113 GLU A 118 1 6 HELIX 4 AA4 PHE A 130 ASN A 134 5 5 HELIX 5 AA5 THR A 143 LYS A 149 1 7 HELIX 6 AA6 ALA A 150 LEU A 152 5 3 HELIX 7 AA7 PRO A 228 ALA A 237 1 10 HELIX 8 AA8 PRO A 274 TYR A 277 5 4 HELIX 9 AA9 GLY A 306 LYS A 311 1 6 SHEET 1 AA1 9 LYS A 68 SER A 78 0 SHEET 2 AA1 9 SER A 84 VAL A 96 -1 O VAL A 89 N LEU A 70 SHEET 3 AA1 9 TYR A 17 ILE A 23 -1 N GLN A 22 O SER A 95 SHEET 4 AA1 9 GLY A 3 PRO A 9 -1 N THR A 8 O ILE A 18 SHEET 5 AA1 9 GLY A 167 PHE A 171 -1 O GLY A 167 N THR A 7 SHEET 6 AA1 9 VAL A 156 ASP A 160 -1 N THR A 158 O ASN A 170 SHEET 7 AA1 9 PHE A 314 ASN A 318 -1 O PHE A 317 N PHE A 157 SHEET 8 AA1 9 THR A 324 ALA A 328 -1 O GLY A 326 N VAL A 316 SHEET 9 AA1 9 THR A 184 ALA A 187 -1 N THR A 184 O PHE A 327 SHEET 1 AA213 LYS A 68 SER A 78 0 SHEET 2 AA213 SER A 84 VAL A 96 -1 O VAL A 89 N LEU A 70 SHEET 3 AA213 LEU A 99 VAL A 112 -1 O VAL A 106 N TYR A 90 SHEET 4 AA213 LEU A 41 VAL A 43 1 N LEU A 41 O GLU A 107 SHEET 5 AA213 GLY A 124 GLY A 127 -1 O LEU A 125 N TRP A 42 SHEET 6 AA213 GLN A 28 ASP A 35 1 N ASP A 33 O GLY A 124 SHEET 7 AA213 TYR A 17 ILE A 23 -1 N ILE A 23 O GLN A 28 SHEET 8 AA213 GLY A 3 PRO A 9 -1 N THR A 8 O ILE A 18 SHEET 9 AA213 GLY A 167 PHE A 171 -1 O GLY A 167 N THR A 7 SHEET 10 AA213 VAL A 156 ASP A 160 -1 N THR A 158 O ASN A 170 SHEET 11 AA213 PHE A 314 ASN A 318 -1 O PHE A 317 N PHE A 157 SHEET 12 AA213 THR A 324 ALA A 328 -1 O GLY A 326 N VAL A 316 SHEET 13 AA213 THR A 184 ALA A 187 -1 N THR A 184 O PHE A 327 SHEET 1 AA3 7 ALA A 269 ILE A 273 0 SHEET 2 AA3 7 PHE A 262 VAL A 266 -1 N PHE A 262 O ILE A 273 SHEET 3 AA3 7 GLU A 196 VAL A 204 -1 N ALA A 203 O THR A 263 SHEET 4 AA3 7 LYS A 210 ALA A 218 -1 O LYS A 210 N TYR A 202 SHEET 5 AA3 7 ASN A 303 PHE A 305 1 O PHE A 305 N ILE A 217 SHEET 6 AA3 7 LEU A 225 LEU A 227 -1 N TYR A 226 O ILE A 304 SHEET 7 AA3 7 ILE A 294 SER A 296 1 O GLN A 295 N LEU A 225 SHEET 1 AA4 4 LYS A 243 SER A 245 0 SHEET 2 AA4 4 GLY A 250 PRO A 254 -1 O GLY A 250 N SER A 245 SHEET 3 AA4 4 SER A 289 GLY A 292 -1 O CYS A 290 N PHE A 253 SHEET 4 AA4 4 ASP A 279 PRO A 282 -1 N GLY A 281 O PHE A 291 SSBOND 1 CYS A 255 CYS A 290 1555 1555 2.04 CISPEP 1 THR A 25 PRO A 26 0 -5.25 CISPEP 2 SER A 137 PRO A 138 0 4.72 SITE 1 AC1 7 VAL A 272 TYR A 277 ALA A 312 SER A 329 SITE 2 AC1 7 LYS A 330 HOH A 525 HOH A 639 SITE 1 AC2 3 THR A 8 HOH A 505 HOH A 620 SITE 1 AC3 6 ALA A 203 VAL A 204 GLY A 207 THR A 208 SITE 2 AC3 6 LYS A 210 HOH A 502 SITE 1 AC4 11 ASP A 35 GLY A 37 TYR A 79 GLY A 80 SITE 2 AC4 11 ASP A 81 LEU A 125 PHE A 194 ASP A 219 SITE 3 AC4 11 GLY A 221 THR A 222 HOH A 585 SITE 1 AC5 5 CYS A 255 ASP A 279 GLY A 281 CYS A 290 SITE 2 AC5 5 HOH A 540 CRYST1 45.329 73.227 53.031 90.00 109.56 90.00 P 1 21 1 2 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 0.022061 0.000000 0.007840 0.00000 SCALE2 0.000000 0.013656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020012 0.00000