HEADER HYDROLASE 11-FEB-11 3QPD TITLE STRUCTURE OF ASPERGILLUS ORYZAE CUTINASE EXPRESSED IN PICHIA PASTORIS, TITLE 2 CRYSTALLIZED IN THE PRESENCE OF PARAOXON COMPND MOL_ID: 1; COMPND 2 MOLECULE: CUTINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 26-212; COMPND 5 SYNONYM: CUTIN HYDROLASE 1, L1; COMPND 6 EC: 3.1.1.74; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS ORYZAE; SOURCE 3 ORGANISM_TAXID: 5062; SOURCE 4 GENE: CUTL, AO090005000029; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS ALPHA-BETA HYDROLASE FOLD, ESTERASE, HYDROLASE, CUTIN, MONO-ETHYL KEYWDS 2 PHOSPHORYLATED SERINE RESIDUE, SECRETED, PHOSPHORYLATED SERINE KEYWDS 3 RESIDUE EXPDTA X-RAY DIFFRACTION AUTHOR A.LU,Y.GOSSER,J.K.MONTCLARE,Z.LIU,X.KONG REVDAT 3 06-NOV-24 3QPD 1 LINK REVDAT 2 14-MAR-12 3QPD 1 AUTHOR REVDAT 1 29-FEB-12 3QPD 0 JRNL AUTH A.LU,Y.GOSSER,J.K.MONTCLARE,Z.LIU,X.KONG JRNL TITL STRUCTURE OF ASPERGILLUS ORYZAE CUTINASE EXPRESSED IN PICHIA JRNL TITL 2 PASTORIS, CRYSTALLIZED IN THE PRESENCE OF PARAOXON JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 26363 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1345 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 37.9060 - 3.3834 0.94 2613 140 0.1580 0.1715 REMARK 3 2 3.3834 - 2.6857 1.00 2606 136 0.1686 0.1961 REMARK 3 3 2.6857 - 2.3463 1.00 2556 133 0.1564 0.1762 REMARK 3 4 2.3463 - 2.1318 1.00 2518 145 0.1466 0.1666 REMARK 3 5 2.1318 - 1.9790 1.00 2537 144 0.1514 0.1807 REMARK 3 6 1.9790 - 1.8623 1.00 2517 139 0.1472 0.1777 REMARK 3 7 1.8623 - 1.7690 0.99 2521 110 0.1450 0.2093 REMARK 3 8 1.7690 - 1.6920 0.99 2484 140 0.1410 0.1747 REMARK 3 9 1.6920 - 1.6269 0.99 2478 128 0.1355 0.1802 REMARK 3 10 1.6269 - 1.5708 0.98 2471 130 0.1386 0.1582 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 : 0.36 REMARK 3 B_SOL : 41.67 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.330 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) : 0.74010 REMARK 3 B22 (A**2) : 0.74010 REMARK 3 B33 (A**2) : -1.99020 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 : 0.014 1418 REMARK 3 ANGLE : 1.570 1929 REMARK 3 CHIRALITY : 0.099 222 REMARK 3 PLANARITY : 0.009 257 REMARK 3 DIHEDRAL : 14.261 529 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 3QPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063934. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.77009 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26363 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 37.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG2KMME, 0.1M POTASSIUM REMARK 280 THIOCYANATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 105.14067 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 52.57033 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 52.57033 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 105.14067 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 409 LIES ON A SPECIAL POSITION. 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 -13.13 77.36 REMARK 500 SER A 57 -100.88 -132.94 REMARK 500 SEP A 126 -122.85 56.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QPC RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF FSC CUTIANSE IN THE PRESENCE OF PAROXON REMARK 900 RELATED ID: 3GBS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ASPERGILLUS ORYZAE CUTINASE REMARK 900 RELATED ID: 3QPA RELATED DB: PDB DBREF 3QPD A 26 212 UNP P52956 CUTI1_ASPOR 26 212 SEQRES 1 A 187 LEU THR GLY GLY ASP GLU LEU ARG ASP GLY PRO CYS LYS SEQRES 2 A 187 PRO ILE THR PHE ILE PHE ALA ARG ALA SER THR GLU PRO SEQRES 3 A 187 GLY LEU LEU GLY ILE SER THR GLY PRO ALA VAL CYS ASN SEQRES 4 A 187 ARG LEU LYS LEU ALA ARG SER GLY ASP VAL ALA CYS GLN SEQRES 5 A 187 GLY VAL GLY PRO ARG TYR THR ALA ASP LEU PRO SER ASN SEQRES 6 A 187 ALA LEU PRO GLU GLY THR SER GLN ALA ALA ILE ALA GLU SEQRES 7 A 187 ALA GLN GLY LEU PHE GLU GLN ALA VAL SER LYS CYS PRO SEQRES 8 A 187 ASP THR GLN ILE VAL ALA GLY GLY TYR SEP GLN GLY THR SEQRES 9 A 187 ALA VAL MET ASN GLY ALA ILE LYS ARG LEU SER ALA ASP SEQRES 10 A 187 VAL GLN ASP LYS ILE LYS GLY VAL VAL LEU PHE GLY TYR SEQRES 11 A 187 THR ARG ASN ALA GLN GLU ARG GLY GLN ILE ALA ASN PHE SEQRES 12 A 187 PRO LYS ASP LYS VAL LYS VAL TYR CYS ALA VAL GLY ASP SEQRES 13 A 187 LEU VAL CYS LEU GLY THR LEU ILE VAL ALA PRO PRO HIS SEQRES 14 A 187 PHE SER TYR LEU SER ASP THR GLY ASP ALA SER ASP PHE SEQRES 15 A 187 LEU LEU SER GLN LEU MODRES 3QPD SEP A 126 SER PHOSPHOSERINE HET SEP A 126 10 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 HOH *237(H2 O) HELIX 1 1 ASP A 30 GLY A 35 1 6 HELIX 2 2 SER A 57 ARG A 70 1 14 HELIX 3 3 ASP A 86 LEU A 92 5 7 HELIX 4 4 SER A 97 CYS A 115 1 19 HELIX 5 5 SEP A 126 LYS A 137 1 12 HELIX 6 6 SER A 140 LYS A 146 1 7 HELIX 7 7 PRO A 169 ASP A 171 5 3 HELIX 8 8 ASP A 181 GLY A 186 5 6 HELIX 9 9 ALA A 191 SER A 199 5 9 HELIX 10 10 ASP A 200 LEU A 212 1 13 SHEET 1 A 5 VAL A 74 GLY A 78 0 SHEET 2 A 5 ILE A 40 ALA A 45 1 N PHE A 42 O ALA A 75 SHEET 3 A 5 GLN A 119 TYR A 125 1 O VAL A 121 N THR A 41 SHEET 4 A 5 ILE A 147 PHE A 153 1 O LYS A 148 N ILE A 120 SHEET 5 A 5 VAL A 173 TYR A 176 1 O TYR A 176 N LEU A 152 SSBOND 1 CYS A 37 CYS A 115 1555 1555 2.06 SSBOND 2 CYS A 63 CYS A 76 1555 1555 2.08 SSBOND 3 CYS A 177 CYS A 184 1555 1555 2.06 LINK C TYR A 125 N SEP A 126 1555 1555 1.33 LINK C SEP A 126 N GLN A 127 1555 1555 1.34 CISPEP 1 GLY A 35 PRO A 36 0 2.03 CISPEP 2 GLY A 80 PRO A 81 0 7.08 CRYST1 45.078 45.078 157.711 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 0.022184 0.012808 0.000000 0.00000 SCALE2 0.000000 0.025616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006341 0.00000