+Open data
-Basic information
Entry | Database: PDB / ID: 2zdi | ||||||
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Title | Crystal structure of Prefoldin from Pyrococcus horikoshii OT3 | ||||||
Components |
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Keywords | CHAPERONE / PREFOLDIN / Cytoplasm | ||||||
Function / homology | Function and homology information prefoldin complex / unfolded protein binding / protein folding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kida, H. / Miki, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins Authors: Ohtaki, A. / Kida, H. / Miyata, Y. / Ide, N. / Yonezawa, A. / Arakawa, T. / Iizuka, R. / Noguchi, K. / Kita, A. / Odaka, M. / Miki, K. / Yohda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zdi.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zdi.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zdi_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 2zdi_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 2zdi_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 2zdi_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/2zdi ftp://data.pdbj.org/pub/pdb/validation_reports/zd/2zdi | HTTPS FTP |
-Related structure data
Related structure data | 1fxkS S: Starting model for refinement |
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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: 13333.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: pfdB / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: O58268 #2: Protein | | Mass: 17027.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: pfdA / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: O58263 #3: Chemical | Sequence details | THE N-TERMINAL 3 RESIDUES (MET, ILE, ARG) OF CHAIN C (ENTITY 2) WERE INCLUDED IN ACCESSION NO. ...THE N-TERMINAL 3 RESIDUES (MET, ILE, ARG) OF CHAIN C (ENTITY 2) WERE INCLUDED IN ACCESSION NO. BA000001-547 OF DDBJ DATABASE, BUT NOT IN ACCESSION NO. O58263 OF UNIPROT DATABASE. | |
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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: 2.89 Å3/Da / Density % sol: 57.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 400, 0.1M Sodium chloride, 0.1M Lithium sulfate, 0.1M MES-NaOH pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-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: Oct 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 10215 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 66.56 Å2 / Rsym value: 0.055 / Net I/σ(I): 25.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FXK Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(I): -3
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Displacement parameters | Biso mean: 59.14 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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