HEADER HYDROLASE 02-MAR-10 3LZY TITLE CRYSTAL STRUCTURE OF ENDOTHIAPESIN IN COMPLEX WITH XENON COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOTHIAPEPSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 90-419; COMPND 5 SYNONYM: ASPARTATE PROTEASE; COMPND 6 EC: 3.4.23.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRYPHONECTRIA PARASITICA; SOURCE 3 ORGANISM_COMMON: CHESNUT BLIGHT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5116 KEYWDS PROTEIN-XE COMPLEX, HYDROLASE, B-SECRETASE, ENDOTHIAPEPSIN, ASPARTYL KEYWDS 2 PROTEASE, PROTEASE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR J.BEHNEN,H.KRUEGER,G.KLEBE,A.HEINE REVDAT 2 08-NOV-17 3LZY 1 REMARK REVDAT 1 25-MAY-11 3LZY 0 JRNL AUTH J.BEHNEN,H.KRUEGER,L.TOKER,B.BRUMSHTEIN,I.SILMAN, JRNL AUTH 2 J.L.SUSSMAN,G.KLEBE,A.HEINE JRNL TITL OLD ACQUANTANCE REDISCOVER: USE OF XENON/PROTEIN COMPLEXES JRNL TITL 2 AS A GENERIC TOOL FOR SAD PHASING OF INHOUSE DATA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.161 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.170 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.155 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 28096 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2373 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2642.6 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2248.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10637 REMARK 3 NUMBER OF RESTRAINTS : 10013 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.041 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.041 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.021 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.051 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 3 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ? REMARK 4 REMARK 4 3LZY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000057933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30406 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24000 REMARK 200 FOR SHELL : 7.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG4000, 200MM AMMONIUM ACETATE, REMARK 280 100 MM NA-ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 288K 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 36.76100 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 CG CD CE NZ REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 LYS A 243 CG CD CE NZ 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 THR A 49 117.84 -38.16 REMARK 500 ALA A 129 -168.35 -78.06 REMARK 500 ALA A 320 173.05 -59.64 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 XE A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2003 DBREF 3LZY 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 XE A1001 1 HET GOL A2001 6 HET GOL A2002 6 HET GOL A2003 6 HETNAM XE XENON HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 XE XE FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 HOH *256(H2 O) HELIX 1 1 THR A 49 VAL A 53 5 5 HELIX 2 2 THR A 60 SER A 64 5 5 HELIX 3 3 SER A 113 GLU A 118 1 6 HELIX 4 4 PHE A 130 ASN A 134 5 5 HELIX 5 5 THR A 143 LYS A 149 1 7 HELIX 6 6 ALA A 150 LEU A 152 5 3 HELIX 7 7 PRO A 228 ALA A 237 1 10 HELIX 8 8 PRO A 274 TYR A 277 5 4 HELIX 9 9 GLY A 306 LYS A 311 1 6 SHEET 1 A 9 LYS A 68 SER A 78 0 SHEET 2 A 9 SER A 84 VAL A 96 -1 O SER A 85 N ILE A 77 SHEET 3 A 9 TYR A 17 ILE A 23 -1 N GLN A 22 O SER A 95 SHEET 4 A 9 GLY A 3 PRO A 9 -1 N THR A 8 O ILE A 18 SHEET 5 A 9 GLY A 167 PHE A 171 -1 O GLY A 167 N THR A 7 SHEET 6 A 9 VAL A 156 ASP A 160 -1 N THR A 158 O ASN A 170 SHEET 7 A 9 PHE A 314 ASN A 318 -1 O PHE A 317 N PHE A 157 SHEET 8 A 9 THR A 324 ALA A 328 -1 O ALA A 328 N PHE A 314 SHEET 9 A 9 THR A 184 ALA A 187 -1 N THR A 184 O PHE A 327 SHEET 1 B13 LYS A 68 SER A 78 0 SHEET 2 B13 SER A 84 VAL A 96 -1 O SER A 85 N ILE A 77 SHEET 3 B13 LEU A 99 VAL A 112 -1 O VAL A 106 N TYR A 90 SHEET 4 B13 LEU A 41 VAL A 43 1 N LEU A 41 O GLU A 107 SHEET 5 B13 GLY A 124 GLY A 127 -1 O LEU A 125 N TRP A 42 SHEET 6 B13 GLN A 28 ASP A 35 1 N ASP A 35 O LEU A 126 SHEET 7 B13 TYR A 17 ILE A 23 -1 N VAL A 21 O LEU A 30 SHEET 8 B13 GLY A 3 PRO A 9 -1 N THR A 8 O ILE A 18 SHEET 9 B13 GLY A 167 PHE A 171 -1 O GLY A 167 N THR A 7 SHEET 10 B13 VAL A 156 ASP A 160 -1 N THR A 158 O ASN A 170 SHEET 11 B13 PHE A 314 ASN A 318 -1 O PHE A 317 N PHE A 157 SHEET 12 B13 THR A 324 ALA A 328 -1 O ALA A 328 N PHE A 314 SHEET 13 B13 THR A 184 ALA A 187 -1 N THR A 184 O PHE A 327 SHEET 1 C 7 ALA A 269 ILE A 273 0 SHEET 2 C 7 PHE A 262 VAL A 266 -1 N PHE A 262 O ILE A 273 SHEET 3 C 7 GLU A 196 VAL A 204 -1 N ALA A 203 O THR A 263 SHEET 4 C 7 LYS A 210 ALA A 218 -1 O LYS A 210 N TYR A 202 SHEET 5 C 7 ASN A 303 PHE A 305 1 O PHE A 305 N ILE A 217 SHEET 6 C 7 LEU A 225 LEU A 227 -1 N TYR A 226 O ILE A 304 SHEET 7 C 7 ILE A 294 SER A 296 1 O GLN A 295 N LEU A 225 SHEET 1 D 4 LYS A 243 SER A 245 0 SHEET 2 D 4 GLY A 250 PRO A 254 -1 O GLY A 250 N SER A 245 SHEET 3 D 4 SER A 289 GLY A 292 -1 O CYS A 290 N PHE A 253 SHEET 4 D 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 -6.65 CISPEP 2 SER A 137 PRO A 138 0 1.97 SITE 1 AC1 2 SER A 199 ILE A 214 SITE 1 AC2 3 ALA A 187 TRP A 197 THR A 198 SITE 1 AC3 4 ASP A 15 THR A 223 LEU A 224 HOH A3003 SITE 1 AC4 8 VAL A 272 PRO A 274 TYR A 277 ALA A 312 SITE 2 AC4 8 SER A 329 LYS A 330 HOH A3049 HOH A3225 CRYST1 45.672 73.522 53.282 90.00 109.85 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 0.021895 0.000000 0.007904 0.00000 SCALE2 0.000000 0.013601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019954 0.00000 MASTER 219 0 4 9 33 0 5 6 0 0 0 26 END