HEADER HYDROLASE 02-OCT-02 1IZD TITLE CRYSTAL STRUCTURE OF ASPERGILLUS ORYZAE ASPARTIC PROTEINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTIC PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-323; COMPND 5 SYNONYM: ASPARTIC PROTEINASE II-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS ORYZAE; SOURCE 3 ORGANISM_TAXID: 5062 KEYWDS SUGAR BINDING, ACID PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KAMITORI,A.OHTAKI,H.INO,M.TAKEUCHI REVDAT 5 27-DEC-23 1IZD 1 HETSYN REVDAT 4 29-JUL-20 1IZD 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 04-OCT-17 1IZD 1 REMARK REVDAT 2 24-FEB-09 1IZD 1 VERSN REVDAT 1 04-MAR-03 1IZD 0 JRNL AUTH S.KAMITORI,A.OHTAKI,H.INO,M.TAKEUCHI JRNL TITL CRYSTAL STRUCTURES OF ASPERGILLUS ORYZAE ASPARTIC PROTEINASE JRNL TITL 2 AND ITS COMPLEX WITH AN INHIBITOR PEPSTATIN AT 1.9 A JRNL TITL 3 RESOLUTION JRNL REF J.MOL.BIOL. V. 326 1503 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12595261 JRNL DOI 10.1016/S0022-2836(03)00078-0 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : CNS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 27237 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 SET) : 0.177 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2720 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3798 REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE : 0.2080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 407 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2391 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 309 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.85000 REMARK 3 B22 (A**2) : 1.26000 REMARK 3 B33 (A**2) : -0.41000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : -0.0 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.06 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.660 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.740 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 60.14 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 5 : LIGAND.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 5 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000005435. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74057 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 38.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4200, AMMONIUM ACETATE SODIUM REMARK 280 ACETATE TRIHYDRATE, PH 5.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 24.68050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.78150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.71050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.78150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.68050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.71050 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 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 ASN A 13 19.16 59.79 REMARK 500 ASP A 77 -5.64 -59.22 REMARK 500 LYS A 304 6.86 -68.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IZE RELATED DB: PDB REMARK 900 1IZE CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEXED WITH REMARK 900 PEPSTATIN DBREF 1IZD A 1 323 UNP Q9URD0 Q9URD0_ASPOR 68 390 SEQRES 1 A 323 ALA ALA THR GLY SER VAL THR THR ASN PRO THR SER ASN SEQRES 2 A 323 ASP GLU GLU TYR ILE THR GLN VAL THR VAL GLY ASP ASP SEQRES 3 A 323 THR LEU GLY LEU ASP PHE ASP THR GLY SER ALA ASP LEU SEQRES 4 A 323 TRP VAL PHE SER SER GLN THR PRO SER SER GLU ARG SER SEQRES 5 A 323 GLY HIS ASP TYR TYR THR PRO GLY SER SER ALA GLN LYS SEQRES 6 A 323 ILE ASP GLY ALA THR TRP SER ILE SER TYR GLY ASP GLY SEQRES 7 A 323 SER SER ALA SER GLY ASP VAL TYR LYS ASP LYS VAL THR SEQRES 8 A 323 VAL GLY GLY VAL SER TYR ASP SER GLN ALA VAL GLU SER SEQRES 9 A 323 ALA GLU LYS VAL SER SER GLU PHE THR GLN ASP THR ALA SEQRES 10 A 323 ASN ASP GLY LEU LEU GLY LEU ALA PHE SER SER ILE ASN SEQRES 11 A 323 THR VAL GLN PRO THR PRO GLN LYS THR PHE PHE ASP ASN SEQRES 12 A 323 VAL LYS SER SER LEU SER GLU PRO ILE PHE ALA VAL ALA SEQRES 13 A 323 LEU LYS HIS ASN ALA PRO GLY VAL TYR ASP PHE GLY TYR SEQRES 14 A 323 THR ASP SER SER LYS TYR THR GLY SER ILE THR TYR THR SEQRES 15 A 323 ASP VAL ASP ASN SER GLN GLY PHE TRP GLY PHE THR ALA SEQRES 16 A 323 ASP GLY TYR SER ILE GLY SER ASP SER SER SER ASP SER SEQRES 17 A 323 ILE THR GLY ILE ALA ASP THR GLY THR THR LEU LEU LEU SEQRES 18 A 323 LEU ASP ASP SER ILE VAL ASP ALA TYR TYR GLU GLN VAL SEQRES 19 A 323 ASN GLY ALA SER TYR ASP SER SER GLN GLY GLY TYR VAL SEQRES 20 A 323 PHE PRO SER SER ALA SER LEU PRO ASP PHE SER VAL THR SEQRES 21 A 323 ILE GLY ASP TYR THR ALA THR VAL PRO GLY GLU TYR ILE SEQRES 22 A 323 SER PHE ALA ASP VAL GLY ASN GLY GLN THR PHE GLY GLY SEQRES 23 A 323 ILE GLN SER ASN SER GLY ILE GLY PHE SER ILE PHE GLY SEQRES 24 A 323 ASP VAL PHE LEU LYS SER GLN TYR VAL VAL PHE ASP ALA SEQRES 25 A 323 SER GLY PRO ARG LEU GLY PHE ALA ALA GLN ALA MODRES 1IZD THR A 3 THR GLYCOSYLATION SITE HET MAN A1001 11 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 MAN C6 H12 O6 FORMUL 3 HOH *309(H2 O) HELIX 1 1 SER A 12 GLU A 15 5 4 HELIX 2 2 PRO A 47 SER A 52 1 6 HELIX 3 3 SER A 109 ASP A 115 1 7 HELIX 4 4 PHE A 126 ASN A 130 5 5 HELIX 5 5 THR A 139 LYS A 145 1 7 HELIX 6 6 SER A 146 LEU A 148 5 3 HELIX 7 7 ASP A 223 GLU A 232 1 10 HELIX 8 8 PRO A 269 ILE A 273 1 5 HELIX 9 9 GLY A 299 LYS A 304 1 6 SHEET 1 A15 GLN A 64 SER A 74 0 SHEET 2 A15 SER A 80 VAL A 92 -1 O ALA A 81 N ILE A 73 SHEET 3 A15 TYR A 17 VAL A 23 -1 O THR A 22 N THR A 91 SHEET 4 A15 ASP A 26 ASP A 33 -1 O ASP A 26 N VAL A 23 SHEET 5 A15 GLY A 120 GLY A 123 1 O GLY A 120 N ASP A 31 SHEET 6 A15 LEU A 39 VAL A 41 -1 O TRP A 40 N LEU A 121 SHEET 7 A15 VAL A 95 VAL A 108 1 N GLU A 103 O LEU A 39 SHEET 8 A15 SER A 80 VAL A 92 -1 O SER A 82 N GLU A 106 SHEET 9 A15 TYR A 17 VAL A 23 -1 O THR A 22 N THR A 91 SHEET 10 A15 GLY A 4 PRO A 10 -1 O THR A 7 N GLN A 20 SHEET 11 A15 GLY A 163 PHE A 167 -1 N GLY A 163 O THR A 8 SHEET 12 A15 ILE A 152 ALA A 156 -1 N ALA A 154 O ASP A 166 SHEET 13 A15 GLN A 306 ASP A 311 -1 N VAL A 308 O VAL A 155 SHEET 14 A15 ARG A 316 GLN A 322 -1 O ARG A 316 N ASP A 311 SHEET 15 A15 TYR A 175 ASP A 183 -1 N THR A 176 O ALA A 321 SHEET 1 B 5 GLY A 192 ALA A 195 0 SHEET 2 B 5 ILE A 209 ALA A 213 -1 O ILE A 209 N ALA A 195 SHEET 3 B 5 SER A 296 PHE A 298 1 O SER A 296 N ILE A 212 SHEET 4 B 5 LEU A 220 LEU A 222 -1 N LEU A 221 O ILE A 297 SHEET 5 B 5 ILE A 287 SER A 289 1 N GLN A 288 O LEU A 220 SHEET 1 C 4 ASP A 203 SER A 205 0 SHEET 2 C 4 GLY A 197 ILE A 200 -1 O TYR A 198 N SER A 205 SHEET 3 C 4 PHE A 257 ILE A 261 -1 O SER A 258 N SER A 199 SHEET 4 C 4 TYR A 264 VAL A 268 -1 O TYR A 264 N ILE A 261 SHEET 1 D 4 SER A 238 ASP A 240 0 SHEET 2 D 4 GLY A 245 PRO A 249 -1 O GLY A 245 N ASP A 240 SHEET 3 D 4 GLN A 282 GLY A 285 -1 N THR A 283 O PHE A 248 SHEET 4 D 4 SER A 274 ASP A 277 -1 N PHE A 275 O PHE A 284 LINK OG1 THR A 3 C1 MAN A1001 1555 1555 1.39 CISPEP 1 GLN A 133 PRO A 134 0 0.22 CISPEP 2 GLY A 314 PRO A 315 0 -0.25 CRYST1 49.361 79.421 93.563 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 0.020259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010688 0.00000