+Open data
-Basic information
Entry | Database: PDB / ID: 2nac | ||||||
---|---|---|---|---|---|---|---|
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: 1.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2nac.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2nac.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nac_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2nac_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 2nac_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 2nac_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/2nac ftp://data.pdbj.org/pub/pdb/validation_reports/na/2nac | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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: (0.53022, -0.52775, -0.66359), 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: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: FDH_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Num. obs: 61933 / % possible obs: 89.7 % / Observed criterion σ(I): 3 / Num. measured all: 308786 / Rmerge(I) obs: 0.058 / Biso Wilson estimate: 13.9 Å2 |
---|---|
Reflection shell | *PLUS % possible obs: 69.3 % / Rmerge(I) obs: 0.129 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→10 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ/ARP / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 73563 / Rfactor all: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.7 Å2 |