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HEADER HYDROLASE 20-FEB-09 3GBS
TITLE CRYSTAL STRUCTURE OF ASPERGILLUS ORYZAE CUTINASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CUTINASE 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 17-213;
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 STRAIN: IFO 4202;
SOURCE 5 GENE: AO090005000029, CUTL;
SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPICZAA
KEYWDS SERINE ESTERASE, ALPHA BETA HYDROLASE, HYDROLASE, SECRETED
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.GOSSER,Z.LU,G.ALEMU,H.LI,X.KONG,Z.LIU,J.MONTCLARE
REVDAT 1 06-OCT-09 3GBS 0
JRNL AUTH Y.GOSSER,Z.LU,G.ALEMU,H.LI,X.KONG,Z.LIU,J.MONTCLARE
JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHT INTO ASPERGILLUS
JRNL TITL 2 ORYZAE CUTINASE: BIOCATALYSTS FOR ESTERS AND
JRNL TITL 3 POLYESTERS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
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 : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.06
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1
REMARK 3 NUMBER OF REFLECTIONS : 19025
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.194
REMARK 3 FREE R VALUE : 0.199
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 1941
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 : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1369
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 269
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) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 1.27
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3GBS COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-09.
REMARK 100 THE RCSB ID CODE IS RCSB051667.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-NOV-07
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 : X4A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.96785
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19394
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 5.000
REMARK 200 R MERGE (I) : 0.04200
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 8.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2
REMARK 200 DATA REDUNDANCY IN SHELL : 4.70
REMARK 200 R MERGE FOR SHELL (I) : 0.07700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 5.300
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: PDB ENTRY 1CEX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.45
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG MME 2000, 0.1M POTASSIUM
REMARK 280 THIOCYANATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 296K
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 104.74067
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 52.37033
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 52.37033
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 104.74067
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER A 17
REMARK 465 PRO A 18
REMARK 465 VAL A 19
REMARK 465 ASP A 20
REMARK 465 LEU A 21
REMARK 465 GLN A 22
REMARK 465 ASP A 23
REMARK 465 ARG A 24
REMARK 465 GLN A 25
REMARK 465 GLY A 213
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 -12.28 75.67
REMARK 500 SER A 57 -98.87 -127.28
REMARK 500 SER A 126 -123.21 58.73
REMARK 500
REMARK 500 REMARK: NULL
DBREF 3GBS A 17 213 UNP P52956 CUTI1_ASPOR 17 213
SEQRES 1 A 197 SER PRO VAL ASP LEU GLN ASP ARG GLN LEU THR GLY GLY
SEQRES 2 A 197 ASP GLU LEU ARG ASP GLY PRO CYS LYS PRO ILE THR PHE
SEQRES 3 A 197 ILE PHE ALA ARG ALA SER THR GLU PRO GLY LEU LEU GLY
SEQRES 4 A 197 ILE SER THR GLY PRO ALA VAL CYS ASN ARG LEU LYS LEU
SEQRES 5 A 197 ALA ARG SER GLY ASP VAL ALA CYS GLN GLY VAL GLY PRO
SEQRES 6 A 197 ARG TYR THR ALA ASP LEU PRO SER ASN ALA LEU PRO GLU
SEQRES 7 A 197 GLY THR SER GLN ALA ALA ILE ALA GLU ALA GLN GLY LEU
SEQRES 8 A 197 PHE GLU GLN ALA VAL SER LYS CYS PRO ASP THR GLN ILE
SEQRES 9 A 197 VAL ALA GLY GLY TYR SER GLN GLY THR ALA VAL MET ASN
SEQRES 10 A 197 GLY ALA ILE LYS ARG LEU SER ALA ASP VAL GLN ASP LYS
SEQRES 11 A 197 ILE LYS GLY VAL VAL LEU PHE GLY TYR THR ARG ASN ALA
SEQRES 12 A 197 GLN GLU ARG GLY GLN ILE ALA ASN PHE PRO LYS ASP LYS
SEQRES 13 A 197 VAL LYS VAL TYR CYS ALA VAL GLY ASP LEU VAL CYS LEU
SEQRES 14 A 197 GLY THR LEU ILE VAL ALA PRO PRO HIS PHE SER TYR LEU
SEQRES 15 A 197 SER ASP THR GLY ASP ALA SER ASP PHE LEU LEU SER GLN
SEQRES 16 A 197 LEU GLY
FORMUL 2 HOH *269(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 LEU A 87 LEU A 92 5 6
HELIX 4 4 SER A 97 CYS A 115 1 19
HELIX 5 5 SER A 126 LYS A 137 1 12
HELIX 6 6 SER A 140 LYS A 146 1 7
HELIX 7 7 ARG A 157 ARG A 162 1 6
HELIX 8 8 PRO A 169 ASP A 171 5 3
HELIX 9 9 ASP A 181 GLY A 186 5 6
HELIX 10 10 ALA A 191 SER A 199 5 9
HELIX 11 11 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 GLN A 77
SHEET 3 A 5 GLN A 119 TYR A 125 1 O GLN A 119 N THR A 41
SHEET 4 A 5 ILE A 147 PHE A 153 1 O PHE A 153 N GLY A 124
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 2.03
SSBOND 2 CYS A 63 CYS A 76 1555 1555 2.03
SSBOND 3 CYS A 177 CYS A 184 1555 1555 2.03
CISPEP 1 GLY A 35 PRO A 36 0 -0.02
CISPEP 2 GLY A 80 PRO A 81 0 0.27
CRYST1 45.299 45.299 157.111 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 0.022076 0.012745 0.000000 0.00000
SCALE2 0.000000 0.025491 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006365 0.00000
TER 1370 LEU A 212
MASTER 257 0 0 11 5 0 0 6 1638 1 6 16
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