HEADER HYDROLASE 30-NOV-05 2D80 TITLE CRYSTAL STRUCTURE OF PHB DEPOLYMERASE FROM PENICILLIUM 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_TAXID: 28572; SOURCE 4 STRAIN: IFO 6345 KEYWDS ALPHA/BETA HYDROLASE FOLD, CIRCULAR PERMUTATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HISANO,K.KASUYA,T.SAITO,T.IWATA,K.MIKI REVDAT 6 23-OCT-24 2D80 1 HETSYN REVDAT 5 29-JUL-20 2D80 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 13-JUL-11 2D80 1 VERSN REVDAT 3 24-FEB-09 2D80 1 VERSN REVDAT 2 21-FEB-06 2D80 1 JRNL REVDAT 1 31-JAN-06 2D80 0 JRNL AUTH T.HISANO,K.KASUYA,Y.TEZUKA,N.ISHII,T.KOBAYASHI,M.SHIRAKI, JRNL AUTH 2 E.OROUDJEV,H.HANSMA,T.IWATA,Y.DOI,T.SAITO,K.MIKI JRNL TITL THE CRYSTAL STRUCTURE OF POLYHYDROXYBUTYRATE DEPOLYMERASE JRNL TITL 2 FROM PENICILLIUM FUNICULOSUM PROVIDES INSIGHTS INTO THE JRNL TITL 3 RECOGNITION AND DEGRADATION OF BIOPOLYESTERS JRNL REF J.MOL.BIOL. V. 356 993 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16405909 JRNL DOI 10.1016/J.JMB.2005.12.028 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) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.660 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.5 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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,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 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 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, 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: 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 SER A 39 -129.26 61.94 REMARK 500 TYR A 52 50.76 -112.31 REMARK 500 ASN A 100 -88.45 -126.36 REMARK 500 VAL A 124 -78.31 -109.10 REMARK 500 LEU A 251 17.73 59.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D81 RELATED DB: PDB REMARK 900 A S39A MUTANT PROTEIN COMPLEXED WITH R3HB TRIMER DBREF 2D80 A 22 330 UNP Q4W9V8 Q4W9V8_ASPFU 66 375 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 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN 2(C6 H12 O6) FORMUL 3 HOH *240(H2 O) 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 1555 1555 2.04 SSBOND 2 CYS A 169 CYS A 180 1555 1555 2.03 SSBOND 3 CYS A 234 CYS A 241 1555 1555 2.03 SSBOND 4 CYS A 250 CYS A 304 1555 1555 2.04 LINK ND2 ASN A 144 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.38 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.39 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.40 LINK O6 BMA B 3 C1 MAN B 5 1555 1555 1.40 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