+Open data
-Basic information
Entry | Database: PDB / ID: 4j8d | ||||||
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Title | Middle domain of Hsc70-interacting protein, crystal form II | ||||||
Components | Hsc70-interacting protein | ||||||
Keywords | CHAPERONE / tetratricopeptide repeat / solenoid / Co-chaperone / cytosol | ||||||
Function / homology | Function and homology information negative regulation of protein refolding / Regulation of HSF1-mediated heat shock response / dATP binding / chaperone cofactor-dependent protein refolding / Hsp70 protein binding / response to bacterium / unfolded protein binding / protein-folding chaperone binding / protein dimerization activity / protein domain specific binding ...negative regulation of protein refolding / Regulation of HSF1-mediated heat shock response / dATP binding / chaperone cofactor-dependent protein refolding / Hsp70 protein binding / response to bacterium / unfolded protein binding / protein-folding chaperone binding / protein dimerization activity / protein domain specific binding / protein-containing complex binding / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Li, Z. / Bracher, A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Structure and function of Hip, an attenuator of the Hsp70 chaperone cycle. Authors: Li, Z. / Hartl, F.U. / Bracher, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j8d.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j8d.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 4j8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j8d_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 4j8d_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 4j8d_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 4j8d_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/4j8d ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j8d | HTTPS FTP |
-Related structure data
Related structure data | 4j8cC 4j8eC 4j8fSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 19761.188 Da / Num. of mol.: 4 / Fragment: UNP residues 78-247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fam10a1, Hip, St13 / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cod+ RIL / References: UniProt: P50503 |
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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: 2.58 Å3/Da / Density % sol: 52.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.15 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9189 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9189 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.8→63.499 Å / Num. all: 19247 / Num. obs: 19247 / % possible obs: 98.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Rsym value: 0.11 / Net I/σ(I): 8.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4J8F Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.643 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1192 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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