| content |
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 Y.GOSSER,A.LU,X.KONG,J.K.MONTCLARE,Z.LIU
REVDAT 1 29-FEB-12 3QPD 0
JRNL AUTH Y.GOSSER,A.LU,X.KONG,J.K.MONTCLARE,Z.LIU
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,VICENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-
REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,
REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL
REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE
REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM
REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,
REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER
REMARK 3 : 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 RCSB ID CODE IS RCSB063934.
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
REMARK 900 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
TER 1389 LEU A 212
MASTER 244 0 1 10 5 0 0 6 1611 1 18 15
END |