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Open data
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Basic information
Entry | Database: PDB / ID: 1fdo | ||||||
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Title | OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI | ||||||
![]() | FORMATE DEHYDROGENASE H | ||||||
![]() | OXIDOREDUCTASE / SELENIUM / SELENOCYSTEINE / SECYS / MOLYBDENUM / MOLYBDOPTERIN / MPT / MOLYBDOPTERIN GUANINE DINUCLEOTIDE / MGD / IRON SULFUR CLUSTER / FE4S4 / FORMATE / DEHYDROGENASE / ANAEROBIC | ||||||
Function / homology | ![]() formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / formate dehydrogenase (NAD+) activity / glucose catabolic process / anaerobic electron transport chain / : / urate catabolic process / molybdopterin cofactor binding ...formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / formate dehydrogenase (NAD+) activity / glucose catabolic process / anaerobic electron transport chain / : / urate catabolic process / molybdopterin cofactor binding / cellular respiration / anaerobic respiration / 4 iron, 4 sulfur cluster binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Sun, P.D. / Boyington, J.C. | ||||||
![]() | ![]() Title: Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Authors: Boyington, J.C. / Gladyshev, V.N. / Khangulov, S.V. / Stadtman, T.C. / Sun, P.D. #1: ![]() Title: Characterization of Crystalline Formate Dehydrogenase H from Escherichia Coli. Stabilization, Epr Spectroscopy, and Preliminary Crystallographic Analysis Authors: Gladyshev, V.N. / Boyington, J.C. / Khangulov, S.V. / Grahame, D.A. / Stadtman, T.C. / Sun, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.3 KB | Display | ![]() |
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PDB format | ![]() | 120.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 994.8 KB | Display | ![]() |
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Full document | ![]() | 1021.5 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 41.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 79465.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: OXIDIZED FORM (MO(VI),FE4S4(OX)) OF FDH-H / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-6MO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion - hanging drop in anaerobic atmosphere pH: 7.5 Details: FDH-H WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION IN AN ANAEROBIC ATMOSPHERE IN THE PRESENCE OF 1.5 M AMMONIUM SULFATE, 1% PEG 400, 20 MM SODIUM FORMATE AND 100 MM HEPES/NAOH AT PH 7.5. ...Details: FDH-H WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION IN AN ANAEROBIC ATMOSPHERE IN THE PRESENCE OF 1.5 M AMMONIUM SULFATE, 1% PEG 400, 20 MM SODIUM FORMATE AND 100 MM HEPES/NAOH AT PH 7.5. PRIOR TO FREEZING IN LIQUID NITROGEN, CRYSTALS WERE OXIDIZED BY SOAKING IN 10 MM BENZYL VIOLOGEN FOR 30 MINUTES., vapor diffusion - hanging drop in anaerobic atmosphere | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 20861 / % possible obs: 93.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.4 / % possible all: 91.4 |
Reflection | *PLUS Num. measured all: 84166 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER ANALYSIS USING PHASES FROM THE STRUCTURE OF REDUCED FDH-H (PDB ENTRY 1AA6) Resolution: 2.8→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 23.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.89 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.231 |