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- PDB-1fqt: CRYSTAL STRUCTURE OF THE RIESKE-TYPE FERREDOXIN ASSOCIATED WITH B... -

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Entry
Database: PDB / ID: 1fqt
TitleCRYSTAL STRUCTURE OF THE RIESKE-TYPE FERREDOXIN ASSOCIATED WITH BIPHENYL DIOXYGENASE
ComponentsRIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE
KeywordsOXIDOREDUCTASE / RIESKE-TYPE FERREDOXIN / 2FE-2S CLUSTER / BETA SANDWICH
Function / homologyRieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulphur domain superfamily / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / aromatic compound catabolic process / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / Biphenyl dioxygenase system ferredoxin subunit
Function and homology information
Specimen sourceBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FE MAD / 1.6 Å resolution
AuthorsColbert, C.L. / Couture, M.M.-J. / Eltis, L.D. / Bolin, J.T.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: A cluster exposed: structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins.
Authors: Colbert, C.L. / Couture, M.M. / Eltis, L.D. / Bolin, J.T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 6, 2000 / Release: Jan 3, 2001
RevisionDateData content typeGroupProviderType
1.0Jan 3, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE
B: RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1307
Polyers24,5022
Non-polymers6285
Water5,657314
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)76.400, 53.100, 64.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE / BIPHENYL DIOXYGENASE / BIPHENYL DIOXYGENASE SYSTEM FERREDOXIN COMPONENT / BIPHENYL DIOXYGENASE


Mass: 12250.814 Da / Num. of mol.: 2 / Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Genus: Burkholderia / Species: Burkholderia xenovoransParaburkholderia xenovorans / Strain: LB400 / Plasmid name: PEBRE12 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P37332, EC: 1.14.12.-
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 / Density percent sol: 52 % / Description: INVERSE BEAM GEOMETRY WAS USED
Crystal growTemp: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG MME 5000, MES buffer, ammonium sulfate, pH 6.3, VAPOR DIFFUSION, SITTING DROP at 283K, pH 6.5
Crystal grow
*PLUS
Temp: 10 ℃ / pH: 7
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
131 mg/mlprotein1drop
20.15 Msodium chloride1drop
31 mMdithiothreitol1drop
420 mMMOPS1drop
525 %mPEG50001reservoir
60.2 Mammonium sulfate1reservoir
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9537,1.742,1.737
DetectorType: ADSC QUANTUM 1 / Details: BENT CYLINDRICAL: SI-MIRROR (RH COATING) / Detector: CCD / Collection date: Apr 10, 1998
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL: MONOCHROMATOR / Diffraction protocol: MULTIPLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.95371.0
21.7421.0
31.7371.0
ReflectionB iso Wilson estimate: 14.5 Å2 / D resolution high: 1.6 Å / D resolution low: 26 Å / Number obs: 34971 / Observed criterion sigma I: 0 / Rmerge I obs: 0.068 / NetI over sigmaI: 9.6 / Redundancy: 4.95 % / Percent possible obs: 98.9
Reflection shellRmerge I obs: 0.412 / Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / MeanI over sigI obs: 2.2 / Redundancy: 4.91 % / Percent possible all: 97.6
Reflection shell
*PLUS
Percent possible obs: 97.6

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: FE MAD
Details: THE GEOMETRY WITHIN THE FE-S CLUSTER AND THE BONDS WITH THE PROTEIN LIGANDS WERE RESTRAINED WITH FORCE CONSTANTS OF: 200 KCAL MOLE^-1 ANG.^2 APPLIED TO FE-S (TARGET=2.28 ANG.), FE-ND1 (2.05 ANG.), AND FE-FE (2.68 ANG.) DISTANCES; 40 KCAL MOLE^-1 RAD^-2 APPLIED TO ANGLES S-FE-ND1 (115 DEG.), S-FE-S (105 DEG.), FE-S-FE (75 DEG.), ND1-FE-ND1 (90 DEG.), FE-ND1-CG (108 DEG.), AND FE-S-CB (109.5 DEG.) REFINEMENT TARGET EQUALS MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: ENGH & HUBER
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 36.83 / Solvent model param ksol: 0.346
Displacement parametersB iso mean: 18.6 Å2 / Aniso B11: -4.24 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 4.28 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.03 Å2
Least-squares processR factor R free: 0.2 / R factor R free error: 0.005 / R factor R work: 0.18 / R factor obs: 0.18 / Highest resolution: 1.6 Å / Lowest resolution: 26 Å / Number reflection R free: 1761 / Number reflection obs: 34933 / Percent reflection R free: 5 / Percent reflection obs: 98.7
Refine analyzeLuzzati coordinate error free: 0.19 Å / Luzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.1 Å / Luzzati sigma a obs: 0.1 Å
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 26 Å
Number of atoms included #LASTProtein: 1674 / Nucleic acid: 0 / Ligand: 26 / Solvent: 314 / Total: 2014
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.96
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.50
X-RAY DIFFRACTIONc_mcangle_it2.292.00
X-RAY DIFFRACTIONc_scbond_it2.452.00
X-RAY DIFFRACTIONc_scangle_it3.652.50
Refine LS shellHighest resolution: 1.6 Å / R factor R free: 0.234 / R factor R free error: 0.014 / R factor R work: 0.225 / Lowest resolution: 1.7 Å / Number reflection R free: 285 / Number reflection R work: 5333 / Total number of bins used: 6 / Percent reflection R free: 5.1 / Percent reflection obs: 96.7
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3FES.PARAMFES.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07

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