+Open data
-Basic information
Entry | Database: PDB / ID: 1aa6 | ||||||
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Title | REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI | ||||||
Components | FORMATE DEHYDROGENASE HFormate dehydrogenase (acceptor) | ||||||
Keywords | OXIDOREDUCTASE / SELENIUM / SELENOCYSTEINE / SECYS / MOLYBDENUM / MOLYBDOPTERIN / MPT / MOLYBDOPTERIN GUANINE DINUCLEOTIDE / MGD / IRON SULFUR CLUSTER / FE4S4 / FORMATE / DEHYDROGENASE / ANAEROBIC | ||||||
Function / homology | Function and homology information formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / plasma membrane respiratory chain complex I / anaerobic electron transport chain / formate dehydrogenase (NAD+) activity / glucose catabolic process / urate catabolic process / anaerobic respiration ...formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / plasma membrane respiratory chain complex I / anaerobic electron transport chain / formate dehydrogenase (NAD+) activity / glucose catabolic process / urate catabolic process / anaerobic respiration / cellular respiration / molybdopterin cofactor binding / 4 iron, 4 sulfur cluster binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 2.3 Å | ||||||
Authors | Sun, P.D. / Boyington, J.C. | ||||||
Citation | Journal: Science / Year: 1997 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: Journal: J.Biol.Chem. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aa6.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aa6.ent.gz | 118.6 KB | Display | PDB format |
PDBx/mmJSON format | 1aa6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/1aa6 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/1aa6 | HTTPS FTP |
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-Related structure data
-Links
-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: REDUCED FORM (MO(IV),FE4S4(RED)) OF FDH-H / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: FM911 / Description: FDH-H WAS EXPRESSED ANAEROBICALLY / Gene: FDHF / Plasmid: PFM20 / Production host: Escherichia coli (E. coli) / References: UniProt: P07658, formate dehydrogenase | ||||
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#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-4MO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion - hanging drop in an 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, vapor diffusion - hanging drop in an 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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0402 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0402 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 36025 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.4 / % possible all: 65 |
Reflection | *PLUS Num. measured all: 169244 |
Reflection shell | *PLUS % possible obs: 65 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR, MAD / Resolution: 2.3→6 Å / Rfactor Rfree error: 0.007 / 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: 28.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.269 |