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HEADER HYDROLASE 30-NOV-05 2D80
TITLE CRYSTAL STRUCTURE OF PHB DEPOLYMERASE FROM PENICILLIUM
TITLE 2 FUNICULOSUM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHB DEPOLYMERASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.1.1.75
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM FUNICULOSUM;
SOURCE 3 ORGANISM_COMMON: FUNGI;
SOURCE 4 STRAIN: IFO 6345
KEYWDS ALPHA/BETA HYDROLASE FOLD, CIRCULAR PERMUTATION
EXPDTA X-RAY DIFFRACTION
AUTHOR T.HISANO,K.KASUYA,T.SAITO,T.IWATA,K.MIKI
REVDAT 1 31-JAN-06 2D80 0
JRNL AUTH T.HISANO,K.KASUYA,Y.TEZUKA,N.ISHII,T.KOBAYASHI,
JRNL AUTH 2 M.SHIRAKI,E.OROUDJEV,H.HANSMA,T.IWATA,Y.DOI,
JRNL AUTH 3 T.SAITO,K.MIKI
JRNL TITL THE CRYSTAL STRUCTURE OF POLYHYDROXYBUTYRATE
JRNL TITL 2 DEPOLYMERASE FROM PENICILLIUM FUNICULOSUM PROVIDES
JRNL TITL 3 INSIGHTS INTO THE RECOGNITION AND DEGRADATION OF
JRNL TITL 4 BIOPOLYESTERS
JRNL REF J.MOL.BIOL. 2006
JRNL REFN ASTM JMOBAK UK ESSN 1089-8638
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.70 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) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.89
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 998709.600
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 27251
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) : 0.174
REMARK 3 FREE R VALUE : 0.204
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2723
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) : 1.70
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4016
REMARK 3 BIN R VALUE (WORKING SET) : 0.2530
REMARK 3 BIN FREE R VALUE : 0.2870
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.90
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 489
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2357
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 61
REMARK 3 SOLVENT ATOMS : 240
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 16.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.31000
REMARK 3 B22 (A**2) : 3.14000
REMARK 3 B33 (A**2) : -5.46000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 2.47000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17
REMARK 3 ESD FROM SIGMAA (A) : 0.17
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) : 0.21
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 0.90
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.66
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) : 0.990 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.350 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.610 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.190 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.38
REMARK 3 BSOL : 42.27
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_DIH
REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM
REMARK 3 PARAMETER FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP_DIH
REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP
REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2D80 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-2005.
REMARK 100 THE RCSB ID CODE IS RCSB025101.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-NOV-2004
REMARK 200 TEMPERATURE (KELVIN) : 90.0
REMARK 200 PH : 6.50
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL44B2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : SI 111
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27251
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
REMARK 200 RESOLUTION RANGE LOW (A) : 38.900
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.07200
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 28.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.36000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 4.640
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 34.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 50MM POTASSIUM
REMARK 280 DIHYDROGENPHOSPHATE, 5% GLYCEROL, PH 6.5, VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 294K
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,1/2+Y,-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 34.43800
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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
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 APPLY THE FOLLOWING TO CHAINS: A, B
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: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 MET A 44 SD MET A 44 CE 0.054
REMARK 500 MET A 115 SD MET A 115 CE -0.054
REMARK 500 MET A 129 SD MET A 129 CE 0.034
REMARK 500 PRO A 158 CG PRO A 158 CD 0.039
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 PRO A 175 C - N - CA ANGL. DEV. = 7.4 DEGREES
REMARK 500 CYS A 250 CA - CB - SG ANGL. DEV. = 6.2 DEGREES
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2D81 RELATED DB: PDB
REMARK 900 A S39A MUTANT PROTEIN COMPLEXED WITH R3HB TRIMER
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES
REMARK 999 NOT CURRENTLY EXIST.
REMARK 999 THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.
SEQRES 1 A 318 THR ALA LEU PRO ALA PHE ASN VAL ASN PRO ASN SER VAL
SEQRES 2 A 318 SER VAL SER GLY LEU SER SER GLY GLY TYR MET ALA ALA
SEQRES 3 A 318 GLN LEU GLY VAL ALA TYR SER ASP VAL PHE ASN VAL GLY
SEQRES 4 A 318 PHE GLY VAL PHE ALA GLY GLY PRO TYR ASP CYS ALA ARG
SEQRES 5 A 318 ASN GLN TYR TYR THR SER CYS MET TYR ASN GLY TYR PRO
SEQRES 6 A 318 SER ILE THR THR PRO THR ALA ASN MET LYS SER TRP SER
SEQRES 7 A 318 GLY ASN GLN ILE ALA SER VAL ALA ASN LEU GLY GLN ARG
SEQRES 8 A 318 LYS ILE TYR MET TRP THR GLY SER SER ASP THR THR VAL
SEQRES 9 A 318 GLY PRO ASN VAL MET ASN GLN LEU LYS ALA GLN LEU GLY
SEQRES 10 A 318 ASN PHE ASP ASN SER ALA ASN VAL SER TYR VAL THR THR
SEQRES 11 A 318 THR GLY ALA VAL HIS THR PHE PRO THR ASP PHE ASN GLY
SEQRES 12 A 318 ALA GLY ASP ASN SER CYS SER LEU SER THR SER PRO TYR
SEQRES 13 A 318 ILE SER ASN CYS ASN TYR ASP GLY ALA GLY ALA ALA LEU
SEQRES 14 A 318 LYS TRP ILE TYR GLY SER LEU ASN ALA ARG ASN THR GLY
SEQRES 15 A 318 THR LEU SER GLY SER VAL LEU SER PHE ALA GLN SER GLY
SEQRES 16 A 318 SER TYR GLY ALA ASN GLY MET ASP THR THR GLY TYR LEU
SEQRES 17 A 318 TYR VAL PRO GLN SER CYS ALA SER GLY ALA THR VAL CYS
SEQRES 18 A 318 SER LEU HIS VAL ALA LEU HIS GLY CYS LEU GLN SER TYR
SEQRES 19 A 318 SER SER ILE GLY SER ARG PHE ILE GLN ASN THR GLY TYR
SEQRES 20 A 318 ASN LYS TRP ALA ASP THR ASN ASN MET ILE ILE LEU TYR
SEQRES 21 A 318 PRO GLN ALA ILE PRO ASP TYR THR ILE HIS ALA ILE TRP
SEQRES 22 A 318 ASN GLY GLY VAL LEU SER ASN PRO ASN GLY CYS TRP ASP
SEQRES 23 A 318 TRP VAL GLY TRP TYR GLY SER ASN ALA ASP GLN ILE GLY
SEQRES 24 A 318 GLY VAL GLN MET ALA ALA ILE VAL GLY GLN VAL LYS GLN
SEQRES 25 A 318 ILE VAL SER GLY PHE GLN
MODRES 2D80 ASN A 144 ASN GLYCOSYLATION SITE
HET NAG B 401 14
HET NAG B 402 14
HET MAN B 403 11
HET MAN B 404 11
HET MAN B 405 11
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETNAM MAN ALPHA-D-MANNOSE
HETSYN NAG NAG
FORMUL 2 NAG 2(C8 H15 N1 O6)
FORMUL 2 MAN 3(C6 H12 O6)
FORMUL 3 HOH *240(H2 O1)
HELIX 1 1 SER A 39 TYR A 52 1 14
HELIX 2 2 TYR A 75 MET A 80 5 6
HELIX 3 3 ILE A 87 SER A 98 1 12
HELIX 4 4 SER A 104 ARG A 111 5 8
HELIX 5 5 GLY A 125 GLY A 137 1 13
HELIX 6 6 ASN A 141 ALA A 143 5 3
HELIX 7 7 ASP A 183 GLY A 194 1 12
HELIX 8 8 SER A 214 GLY A 218 5 5
HELIX 9 9 PRO A 231 SER A 236 1 6
HELIX 10 10 SER A 253 GLY A 258 1 6
HELIX 11 11 SER A 259 THR A 265 1 7
HELIX 12 12 GLY A 266 ASP A 272 1 7
HELIX 13 13 GLY A 320 SER A 335 1 16
SHEET 1 A 8 VAL A 145 THR A 150 0
SHEET 2 A 8 LYS A 112 GLY A 118 1 N MET A 115 O VAL A 148
SHEET 3 A 8 GLY A 59 PHE A 63 1 N VAL A 62 O TYR A 114
SHEET 4 A 8 VAL A 28 LEU A 38 1 N GLY A 37 O PHE A 63
SHEET 5 A 8 CYS A 241 LEU A 247 1 O LEU A 247 N SER A 36
SHEET 6 A 8 MET A 276 TYR A 280 1 O LEU A 279 N ALA A 246
SHEET 7 A 8 THR A 225 VAL A 230 -1 N TYR A 227 O TYR A 280
SHEET 8 A 8 SER A 207 ALA A 212 -1 N PHE A 211 O GLY A 226
SHEET 1 B 2 PHE A 157 THR A 159 0
SHEET 2 B 2 ILE A 177 ASN A 179 1 O SER A 178 N PHE A 157
SHEET 1 C 2 ASP A 286 ALA A 291 0
SHEET 2 C 2 VAL A 297 ASN A 300 -1 O LEU A 298 N HIS A 290
SSBOND 1 CYS A 70 CYS A 79
SSBOND 2 CYS A 169 CYS A 180
SSBOND 3 CYS A 234 CYS A 241
SSBOND 4 CYS A 250 CYS A 304
LINK ND2 ASN A 144 C1 NAG B 401
LINK O4 NAG B 401 C1 NAG B 402
LINK O4 NAG B 402 C1 MAN B 403
LINK O6 MAN B 403 C1 MAN B 405
LINK O3 MAN B 403 C1 MAN B 404
CISPEP 1 SER A 174 PRO A 175 0 0.41
CRYST1 49.507 68.876 38.733 90.00 107.86 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 0.020199 0.000000 0.006510 0.00000
SCALE2 0.000000 0.014519 0.000000 0.00000
SCALE3 0.000000 0.000000 0.027125 0.00000
TER 2358 GLN A 338
MASTER 251 0 5 13 12 0 0 6 2658 1 70 25
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