+Open data
-Basic information
Entry | Database: PDB / ID: 2nad | ||||||
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Title | HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE | ||||||
Components | NAD-DEPENDENT FORMATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE(ALDEHYDE(D) / NAD+(A)) | ||||||
Function / homology | Function and homology information formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.05 Å | ||||||
Authors | Lamzin, V.S. / Dauter, Z. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: High resolution structures of holo and apo formate dehydrogenase. Authors: Lamzin, V.S. / Dauter, Z. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S. #1: Journal: Eur.J.Biochem. / Year: 1992 Title: Crystal Structure of Nad-Dependent Formate Dehydrogenase Authors: Lamzin, V.S. / Aleshin, A.E. / Strokopytov, B.V. / Yukhnevich, M.G. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nad.cif.gz | 180.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nad.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 2nad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/2nad ftp://data.pdbj.org/pub/pdb/validation_reports/na/2nad | 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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Atom site foot note | 1: CIS PROLINE - PRO A 312 / 2: CIS PROLINE - PRO A 314 / 3: CIS PROLINE - PRO B 312 / 4: CIS PROLINE - PRO B 314 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.71486, -0.62783, -0.3079), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 43286.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: 101 / References: UniProt: P33160, formate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: FDH_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.84 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 51142 / % possible obs: 90.3 % / Observed criterion σ(I): 3 / Num. measured all: 206376 / Rmerge(I) obs: 0.045 / Biso Wilson estimate: 11.1 Å2 |
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Reflection shell | *PLUS % possible obs: 84.7 % / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Resolution: 2.05→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.05→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ/ARP / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 50775 / Rfactor all: 0.114 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.4 Å2 |