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Yorodumi- PDB-1d4o: CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d4o | ||||||
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Title | CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS RESOLUTION | ||||||
Components | NADP(H) TRANSHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NUCLEOTIDE-BINDING FOLD / PROTEIN-NADP(H) COMPLEX / INVERTED BINDING OF NADP(H) | ||||||
Function / homology | Function and homology information Citric acid cycle (TCA cycle) / NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / proton transmembrane transport / reactive oxygen species metabolic process / NAD binding / NADP binding / mitochondrial inner membrane / membrane => GO:0016020 / mitochondrion Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.21 Å | ||||||
Authors | Prasad, G.S. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of transhydrogenase domain III at 1.2 A resolution. Authors: Prasad, G.S. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d4o.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d4o.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/1d4o ftp://data.pdbj.org/pub/pdb/validation_reports/d4/1d4o | 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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-Components
#1: Protein | Mass: 20018.066 Da / Num. of mol.: 1 / Fragment: NADP(H) BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cellular location: MITOCHONDRIAMitochondrion / Production host: Escherichia coli (E. coli) / References: UniProt: P11024, EC: 1.6.1.1 |
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#2: Chemical | ChemComp-NAP / |
#3: 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: 2.13 Å3/Da / Density % sol: 42.15 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 24% w/v MPEG 5000, 100mM sodium cacodylate and 200mM magnesium acetate., pH 7.4, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→54.1 Å / Num. all: 89452 / Num. obs: 45717 / % possible obs: 91.2 % / Observed criterion σ(I): 2.3 / Redundancy: 2 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.21→1.24 Å / Redundancy: 91.2 % / Rmerge(I) obs: 0.301 / Num. unique all: 2682 / % possible all: 72.3 |
Reflection | *PLUS Num. measured all: 89452 |
Reflection shell | *PLUS % possible obs: 72.3 % / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Resolution: 1.21→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Shelx least squares procedure.
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Refinement step | Cycle: LAST / Resolution: 1.21→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 3 % / Rfactor Rwork: 0.167 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 1.7 |