+Open data
-Basic information
Entry | Database: PDB / ID: 3vyr | ||||||
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Title | Crystal structure of the HypC-HypD complex | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / [NiFe] hydrogenase maturation | ||||||
Function / homology | Function and homology information carbon dioxide binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Watanabe, S. / Miki, K. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation Authors: Watanabe, S. / Matsumi, R. / 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 | 3vyr.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vyr.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vyr ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vyr | HTTPS FTP |
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-Related structure data
Related structure data | 3vysC 3vytC 3vyuC 2z1dS 2z2cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8133.478 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: Tk-hypC / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII0 | ||||
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#2: Protein | Mass: 41925.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: Tk-hypD / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII1 | ||||
#3: Chemical | ChemComp-CIT / #4: Chemical | ChemComp-SF4 / | #5: 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: 4.68 Å3/Da / Density % sol: 73.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 1.4M (NH4)3 citrate/citric acid(pH 4.5-4.7), 0.7% 2-methyl-2,4-pentandiol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 30506 / Num. obs: 30506 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 45.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.482 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z2C, 2Z1D Resolution: 2.55→45.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1746755.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.7863 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→45.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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