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- PDB-1fdi: OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED W... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fdi | ||||||
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Title | OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED WITH THE INHIBITOR NITRITE | ||||||
![]() | 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 | ![]() | 155.6 KB | Display | ![]() |
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PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 991 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 43.6 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#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 COMPLEXED WITH NITRITE Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 67 molecules ![](data/chem/img/NO2.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/6MO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/6MO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NO2 / | ||||
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#3: Chemical | ChemComp-SF4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-6MO / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 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 AND COMPLEXED WITH NITRITE BY SOAKING IN 10 MM BENZYL VIOLOGEN AND 30 MM SODIUM NITRITE 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: Dec 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: 2.9→50 Å / Num. obs: 19946 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6.9 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 94068 |
Reflection shell | *PLUS % possible obs: 99 % |
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Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER ANALYSIS USING PHASES FROM THE STRUCTURE OF OXIDIZED FDH-H (PDB ENTRY 1FDO) Resolution: 2.9→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: 25.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.99 Å / Rfactor Rfree error: 0.04 / 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: 0.223 |