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Yorodumi- PDB-2iv2: Reinterpretation of reduced form of formate dehydrogenase H from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iv2 | ||||||
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Title | Reinterpretation of reduced form of formate dehydrogenase H from E. coli | ||||||
Components | Formate dehydrogenase HFormate dehydrogenase (acceptor) | ||||||
Keywords | OXIDOREDUCTASE / 4FE-4S / NAEROBIC / DEHYDROGENASE / FE4S4 / FORMATE / IRON / IRON SULFUR CLUSTER / IRON-SULFUR / METAL-BINDING / MGD / MOLYBDENUM / MOLYBDOPTERIN / MOLYBDOPTERIN GUANINE DINUCLEOTIDE / MPT / NAD / SECYS / SELENIUM / SELENOCYSTEINE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Raaijmakers, H.C.A. / Romao, M.J. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2006 Title: Formate-Reduced E. Coli Formate Dehydrogenase H: The Reinterpretation of the Crystal Structure Suggests a New Reaction Mechanism. Authors: Raaijmakers, H.C.A. / Romao, M.J. #1: 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. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iv2.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iv2.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 2iv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2iv2 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2iv2 | HTTPS FTP |
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-Related structure data
Related structure data | 1aa6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules X
#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) / Description: FDH-H WAS EXPRESSED ANAEROBICALLY / Gene: fdhF, b4079, JW4040 / Production host: Escherichia coli (E. coli) References: UniProt: P07658, formate dehydrogenase, EC: 1.17.99.7 |
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-Non-polymers , 6 types, 272 molecules
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-2MD / |
#4: Chemical | ChemComp-MGD / |
#5: Chemical | ChemComp-MO / |
#6: Chemical | ChemComp-UNX / |
#7: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THE RESIDUE X 804 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. AS PART OF REMEDIATION, THIS ...THE RESIDUE X 804 WAS ORIGINALLY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 56 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1AA6. |
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Crystal grow | Details: SEE 1AA6 |
-Data collection
Diffraction source | Source: SYNCHROTRON |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AA6 Resolution: 2.27→34.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.984 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A REINTERPRETATION OF ENTRY 1AA6. THE MAIN DIFFERENCES ARE LOCATED IN RESIDUES 138-146. 297-302 HAVE BEEN REMODELED AS WELL, BUT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A REINTERPRETATION OF ENTRY 1AA6. THE MAIN DIFFERENCES ARE LOCATED IN RESIDUES 138-146. 297-302 HAVE BEEN REMODELED AS WELL, BUT MIGHT BE PARTIALLY IN THE OLD (1AA6) CONFORMATION. POOR FIT FOR RESIDUES 408-412, 631-632, 653-657
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.27→34.5 Å
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