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Yorodumi- PDB-2z1d: Crystal structure of [NiFe] hydrogenase maturation protein, HypD ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z1d | ||||||
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Title | Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis | ||||||
Components | Hydrogenase expression/formation protein hypD | ||||||
Keywords | METAL BINDING PROTEIN / [NiFe] hydrogenase maturation / [4Fe-4S] cluster / thiol redox | ||||||
Function / homology | Function and homology information carbon monoxide binding / protein maturation / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å | ||||||
Authors | Watanabe, S. / Matsumi, R. / Arai, T. / Atomi, H. / Imanaka, T. / Miki, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling Authors: Watanabe, S. / Matsumi, R. / Arai, T. / Atomi, H. / Imanaka, T. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z1d.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z1d.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 2z1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/2z1d ftp://data.pdbj.org/pub/pdb/validation_reports/z1/2z1d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is monomer and the asymmetric unit contains two biological units |
-Components
#1: Protein | Mass: 41957.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: hypD / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII1 #2: Chemical | #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: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 80mM Tris-HCl, 160mM MgCl, 20% PEG4000, 20% ethyleneglycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 47481 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.07→2.14 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.254 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.07→41.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1556566.69 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.0262 Å2 / ksol: 0.345993 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.07→41.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.2 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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