HEADER OXIDOREDUCTASE 13-FEB-07 2ECR TITLE CRYSTAL STRUCTURE OF THE LIGAND-FREE FORM OF THE FLAVIN REDUCTASE TITLE 2 COMPONENT (HPAC) OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVIN REDUCTASE COMPONENT (HPAC) OF 4-HYDROXYPHENYLACETATE COMPND 3 3-MONOOXYGENASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: HYPOTHETICAL PROTEIN TTHA0961; COMPND 6 EC: 1.6.8.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 GENE: TTHA0961; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS FLAVIN REDUCTASE, FLAVIN DIFFUSIBLE, TWO-COMPONENT MONOOXYGENASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.H.KIM,T.HISANO,W.IWASAKI,A.EBIHARA,K.MIKI REVDAT 5 03-APR-24 2ECR 1 REMARK REVDAT 4 10-NOV-21 2ECR 1 SEQADV REVDAT 3 13-JUL-11 2ECR 1 VERSN REVDAT 2 24-FEB-09 2ECR 1 VERSN REVDAT 1 15-JAN-08 2ECR 0 JRNL AUTH S.H.KIM,T.HISANO,W.IWASAKI,A.EBIHARA,K.MIKI JRNL TITL CRYSTAL STRUCTURE OF THE FLAVIN REDUCTASE COMPONENT (HPAC) JRNL TITL 2 OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE FROM THERMUS JRNL TITL 3 THERMOPHILUS HB8: STRUCTURAL BASIS FOR THE FLAVIN AFFINITY JRNL REF PROTEINS V. 70 718 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 17729270 JRNL DOI 10.1002/PROT.21534 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.H.KIM,H.MIYATAKE,T.HISANO,N.OHTANI,K.MIKI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF THE SMALL REMARK 1 TITL 2 COMPONENT OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAC) REMARK 1 TITL 3 AND ITS COFACTOR COMPLEX FROM THERMUS THERMOPHILUS HB8 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 2275 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 14646093 REMARK 1 DOI 10.1107/S0907444903020821 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 5.0 REMARK 3 NUMBER OF REFLECTIONS : 32289 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) : 0.181 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1750 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2241 REMARK 3 BIN FREE R VALUE : 0.2634 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 252 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 : 2260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 304 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30500 REMARK 3 B22 (A**2) : -0.58400 REMARK 3 B33 (A**2) : 0.89000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.33800 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) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 30.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.350 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 2ECR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000026504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35392 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: ARP/WARP REMARK 200 STARTING MODEL: SELENOMETHIONINE-LABELED CRYSTAL WAS USED FOR REMARK 200 PHASE DETERMINATION, AND THE MODEL WAS USED FOR INITIAL TARGET REMARK 200 MODEL. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 4000, 5% ISOPROPYL ALCOHOL, REMARK 280 0.1M HEPES-NAOH, 10% GLYCEROL, PH 7.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 22.00700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL 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 LEU B 38 -50.69 -128.51 REMARK 500 PRO B 85 139.25 -37.12 REMARK 500 TRP B 147 67.73 -153.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ECU RELATED DB: PDB REMARK 900 RELATED ID: 2ED4 RELATED DB: PDB DBREF 2ECR A 1 149 UNP Q5SJP7 Q5SJP7_THET8 1 149 DBREF 2ECR B 1 149 UNP Q5SJP7 Q5SJP7_THET8 1 149 SEQADV 2ECR GLY A 131 UNP Q5SJP7 GLU 131 ENGINEERED MUTATION SEQADV 2ECR GLY B 131 UNP Q5SJP7 GLU 131 ENGINEERED MUTATION SEQRES 1 A 149 MET LYS GLU ALA PHE LYS GLU ALA LEU ALA ARG PHE ALA SEQRES 2 A 149 SER GLY VAL THR VAL VAL ALA ALA ARG LEU GLY GLU GLU SEQRES 3 A 149 GLU ARG GLY MET THR ALA THR ALA PHE MET SER LEU SER SEQRES 4 A 149 LEU GLU PRO PRO LEU VAL ALA LEU ALA VAL SER GLU ARG SEQRES 5 A 149 ALA LYS LEU LEU PRO VAL LEU GLU GLY ALA GLY ALA PHE SEQRES 6 A 149 THR VAL SER LEU LEU ARG GLU GLY GLN GLU ALA VAL SER SEQRES 7 A 149 GLU HIS PHE ALA GLY ARG PRO LYS GLU GLY ILE ALA LEU SEQRES 8 A 149 GLU GLU GLY ARG VAL LYS GLY ALA LEU ALA VAL LEU ARG SEQRES 9 A 149 CYS ARG LEU HIS ALA LEU TYR PRO GLY GLY ASP HIS ARG SEQRES 10 A 149 ILE VAL VAL GLY LEU VAL GLU GLU VAL GLU LEU GLY GLU SEQRES 11 A 149 GLY GLY PRO PRO LEU VAL TYR PHE GLN ARG GLY TYR ARG SEQRES 12 A 149 ARG LEU VAL TRP PRO SER SEQRES 1 B 149 MET LYS GLU ALA PHE LYS GLU ALA LEU ALA ARG PHE ALA SEQRES 2 B 149 SER GLY VAL THR VAL VAL ALA ALA ARG LEU GLY GLU GLU SEQRES 3 B 149 GLU ARG GLY MET THR ALA THR ALA PHE MET SER LEU SER SEQRES 4 B 149 LEU GLU PRO PRO LEU VAL ALA LEU ALA VAL SER GLU ARG SEQRES 5 B 149 ALA LYS LEU LEU PRO VAL LEU GLU GLY ALA GLY ALA PHE SEQRES 6 B 149 THR VAL SER LEU LEU ARG GLU GLY GLN GLU ALA VAL SER SEQRES 7 B 149 GLU HIS PHE ALA GLY ARG PRO LYS GLU GLY ILE ALA LEU SEQRES 8 B 149 GLU GLU GLY ARG VAL LYS GLY ALA LEU ALA VAL LEU ARG SEQRES 9 B 149 CYS ARG LEU HIS ALA LEU TYR PRO GLY GLY ASP HIS ARG SEQRES 10 B 149 ILE VAL VAL GLY LEU VAL GLU GLU VAL GLU LEU GLY GLU SEQRES 11 B 149 GLY GLY PRO PRO LEU VAL TYR PHE GLN ARG GLY TYR ARG SEQRES 12 B 149 ARG LEU VAL TRP PRO SER FORMUL 3 HOH *304(H2 O) HELIX 1 1 LYS A 2 ALA A 10 1 9 HELIX 2 2 LYS A 54 GLY A 63 1 10 HELIX 3 3 GLN A 74 PHE A 81 1 8 HELIX 4 4 LYS B 2 ALA B 10 1 9 HELIX 5 5 LYS B 54 GLY B 63 1 10 HELIX 6 6 GLN B 74 PHE B 81 1 8 SHEET 1 A 3 SER A 14 GLY A 15 0 SHEET 2 A 3 VAL A 136 TYR A 137 -1 O TYR A 137 N SER A 14 SHEET 3 A 3 TYR A 142 ARG A 143 -1 O ARG A 143 N VAL A 136 SHEET 1 B 7 GLU A 26 ALA A 32 0 SHEET 2 B 7 THR A 17 LEU A 23 -1 N VAL A 19 O MET A 30 SHEET 3 B 7 ALA A 64 LEU A 69 -1 O THR A 66 N ALA A 20 SHEET 4 B 7 ALA A 101 GLY A 113 -1 O CYS A 105 N PHE A 65 SHEET 5 B 7 HIS A 116 LEU A 128 -1 O ILE A 118 N TYR A 111 SHEET 6 B 7 LEU A 44 SER A 50 -1 N LEU A 47 O VAL A 119 SHEET 7 B 7 PHE A 35 SER A 39 -1 N MET A 36 O ALA A 46 SHEET 1 C 3 SER B 14 GLY B 15 0 SHEET 2 C 3 VAL B 136 PHE B 138 -1 O TYR B 137 N SER B 14 SHEET 3 C 3 GLY B 141 ARG B 143 -1 O ARG B 143 N VAL B 136 SHEET 1 D 7 GLU B 26 ALA B 32 0 SHEET 2 D 7 THR B 17 LEU B 23 -1 N VAL B 19 O MET B 30 SHEET 3 D 7 ALA B 64 LEU B 69 -1 O THR B 66 N ALA B 20 SHEET 4 D 7 ALA B 101 GLY B 113 -1 O CYS B 105 N PHE B 65 SHEET 5 D 7 HIS B 116 LEU B 128 -1 O ILE B 118 N TYR B 111 SHEET 6 D 7 LEU B 44 SER B 50 -1 N LEU B 47 O VAL B 119 SHEET 7 D 7 PHE B 35 SER B 39 -1 N MET B 36 O ALA B 46 CISPEP 1 GLU A 41 PRO A 42 0 0.05 CISPEP 2 TRP A 147 PRO A 148 0 0.24 CISPEP 3 GLU B 41 PRO B 42 0 -0.33 CRYST1 41.455 44.014 74.930 90.00 92.89 90.00 P 1 21 1 4 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 0.024123 0.000000 0.001218 0.00000 SCALE2 0.000000 0.022720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013363 0.00000