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Yorodumi- PDB-1qp8: CRYSTAL STRUCTURE OF A PUTATIVE FORMATE DEHYDROGENASE FROM PYROBA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qp8 | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE FORMATE DEHYDROGENASE FROM PYROBACULUM AEROPHILUM | ||||||
Components | FORMATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / SIMILAR TO THE PREVIOUSLY SOLVED FORMATE DEHYDROGENASE | ||||||
Function / homology | Function and homology information hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrobaculum aerophilum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Peat, T.S. / Newman, J. / Waldo, G.S. / Terwilliger, T.C. | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of a Putative Formate Dehydrogenase from Pyrobaculum Aerophilum Authors: Peat, T.S. / Newman, J. / Waldo, G.S. / Terwilliger, T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qp8.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qp8.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qp8 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qp8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit has two molecules, A and B. The A molecule is bound to NADP, whereas there is no density for the NADP in the B molecule. The A molecule is also much better ordered than the B molecule in the small domain. |
-Components
#1: Protein | Mass: 34026.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FULL LENGTH PROTEIN WITH C-TERM HIS TAG (HHHHHH). HIS TAG WAS NOT SEEN IN THE DENSITY. Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Description: hyperthermophilic archeabacterium / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZXP5 #2: Chemical | ChemComp-NDP / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: about 3M formate at pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 28370 / Num. obs: 28352 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.8→3 Å / Redundancy: 16 % / Rmerge(I) obs: 0.31 / Num. unique all: 4754 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.8→50 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The bulk solvent was used as implemented in CNS.
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Displacement parameters | Biso mean: 59.2 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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