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Yorodumi- PDB-1fqt: CRYSTAL STRUCTURE OF THE RIESKE-TYPE FERREDOXIN ASSOCIATED WITH B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fqt | ||||||
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Title | CRYSTAL STRUCTURE OF THE RIESKE-TYPE FERREDOXIN ASSOCIATED WITH BIPHENYL DIOXYGENASE | ||||||
Components | RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / RIESKE-TYPE FERREDOXIN / 2FE-2S CLUSTER / BETA SANDWICH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia xenovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FE MAD / Resolution: 1.6 Å | ||||||
Authors | Colbert, C.L. / Couture, M.M.-J. / Eltis, L.D. / Bolin, J.T. | ||||||
Citation | Journal: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fqt.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fqt.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fqt ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fqt | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12250.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Plasmid: PEBRE12 / Production host: Escherichia coli (E. coli) References: UniProt: P37332, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 52 % / Description: INVERSE BEAM GEOMETRY WAS USED | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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 Temperature: 10 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9537,1.742,1.737 | ||||||||||||
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 10, 1998 / Details: BENT CYLINDRICAL: SI-MIRROR (RH COATING) | ||||||||||||
Radiation | Monochromator: SI(111) DOUBLE-CRYSTAL: MONOCHROMATOR / Protocol: MULTIPLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→26 Å / Num. obs: 34971 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.95 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.6 | ||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.91 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.2 / % possible all: 97.6 | ||||||||||||
Reflection shell | *PLUS % possible obs: 97.6 % |
-Processing
Software |
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Refinement | Method to determine structure: FE MAD / Resolution: 1.6→26 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER 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 ...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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.83 Å2 / ksol: 0.346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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