+Open data
-Basic information
Entry | Database: PDB / ID: 2och | ||||||
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Title | J-domain of dnj-12 from Caenorhabditis elegans | ||||||
Components | Hypothetical protein dnj-12Hypothesis | ||||||
Keywords | CHAPERONE / hsp40 / J-domain / APC90013.2 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / heat shock protein binding / unfolded protein binding / protein folding / response to heat / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Osipiuk, J. / Maltseva, N. / Gu, M. / Voisine, C. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of J-domain of dnj-12 from Caenorhabditis elegans. Authors: Osipiuk, J. / Maltseva, N. / Gu, M. / Voisine, C. / Morimoto, R.I. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2och.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2och.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 2och.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/2och ftp://data.pdbj.org/pub/pdb/validation_reports/oc/2och | HTTPS FTP |
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-Related structure data
Related structure data | 2o37 S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN. THIS ENTRY CONTAINS THE N-TERMINAL DOMAIN ONLY. C-TERMINAL DOMAIN IS RESPONSIBLE FOR DIMERIZATION IN THE FULL LENGTH PROTEIN |
-Components
#1: Protein | Mass: 8355.271 Da / Num. of mol.: 1 / Fragment: residues 1-70 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dnj-12 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O45502 |
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#2: 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: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 21, 2006 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→34.5 Å / Num. all: 7363 / Num. obs: 7363 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 3.04 / Num. unique all: 604 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O37 PDB ENTRY 2o37 Resolution: 1.86→34.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.518 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.324 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→34.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.855→1.903 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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