HEADER HYDROLASE 10-APR-24 7H5H TITLE CRYSTAL STRUCTURE OF ENDOTHIAPEPSIN PF_RT2 IN COMPLEX WITH AC40075 AT TITLE 2 296 K 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 ENDOPEPTIDASE, HYDROLASE, ROOM TEMPERATURE EXPDTA X-RAY DIFFRACTION AUTHOR C.-Y.HUANG,S.AUMONIER,V.OLIERIC,M.WANG REVDAT 3 13-NOV-24 7H5H 1 REMARK REVDAT 2 21-AUG-24 7H5H 1 JRNL REVDAT 1 07-AUG-24 7H5H 0 JRNL AUTH C.Y.HUANG,S.AUMONIER,V.OLIERIC,M.WANG JRNL TITL CRYO2RT: A HIGH-THROUGHPUT METHOD FOR ROOM-TEMPERATURE JRNL TITL 2 MACROMOLECULAR CRYSTALLOGRAPHY FROM CRYO-COOLED CRYSTALS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 80 620 2024 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 39052318 JRNL DOI 10.1107/S2059798324006697 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.4 (23-JAN-2024) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26685 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1335 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 : 51 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.21 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 534 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3454 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 507 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE : 0.3529 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.06 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 27 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2379 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.68580 REMARK 3 B22 (A**2) : 5.39980 REMARK 3 B33 (A**2) : -4.71410 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.95220 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.220 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.141 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.128 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.139 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.127 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2514 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3417 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 737 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 412 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2514 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 357 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1936 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.47 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7H5H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-24. REMARK 100 THE DEPOSITION ID IS D_1001407048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-23 REMARK 200 TEMPERATURE (KELVIN) : 296 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA 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 : 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 : 26685 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 43.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.960 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.06 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE PH 4.6, AND 26 - 30% (V/V) PEG 4000, VAPOR DIFFUSION, REMARK 280 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 36.92200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 63 CE NZ REMARK 470 LYS A 142 NZ REMARK 470 LYS A 149 NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 LYS A 243 CE NZ DBREF 7H5H 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 ACT A 901 4 HET DMS A 902 4 HET DMS A 903 4 HET DMS A 904 4 HET DMS A 905 4 HET DMS A 906 4 HET DMS A 907 4 HET DMS A 908 4 HET DMS A 909 4 HET DMS A 910 4 HET DMS A 911 4 HET DMS A 912 4 HET DMS A 913 4 HET DMS A 914 4 HET DMS A 915 4 HET DMS A 916 4 HET DMS A 917 4 HET DMS A 918 4 HET DMS A 919 4 HET DMS A 920 4 HET DMS A 921 4 HET DMS A 922 4 HET DMS A 923 4 HET DMS A 924 4 HET DMS A 925 4 HET DMS A 926 4 HET DMS A 927 4 HETNAM ACT ACETATE ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 DMS 26(C2 H6 O S) FORMUL 29 HOH *159(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 ASP A 119 1 7 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 ALA A 328 N PHE A 314 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 PHE A 44 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 35 O LEU A 126 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 ALA A 328 N PHE A 314 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 GLY A 216 N TRP A 197 SHEET 5 AA3 7 ILE A 304 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 -5.34 CISPEP 2 SER A 137 PRO A 138 0 -1.39 CRYST1 45.804 73.844 52.957 90.00 109.23 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 0.021832 0.000000 0.007616 0.00000 SCALE2 0.000000 0.013542 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019999 0.00000