+Open data
-Basic information
Entry | Database: PDB / ID: 4hel | ||||||
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Title | Crystal structure analysis of apo-GroEL structure | ||||||
Components | 60 kDa chaperonin 4 | ||||||
Keywords | CHAPERONE / GroEL / Assist in protein folding / GroES | ||||||
Function / homology | Function and homology information mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / chaperonin ATPase / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production ...mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / chaperonin ATPase / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of T cell activation / unfolded protein binding / protein-folding chaperone binding / protein refolding / response to heat / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Saxena, A.K. / Meena, S.R. | ||||||
Citation | Journal: To be Published Title: Crystal structure of apo-GroEL structure Authors: Meena, S.R. / Saxena, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hel.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4hel.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 4hel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hel_validation.pdf.gz | 540.7 KB | Display | wwPDB validaton report |
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Full document | 4hel_full_validation.pdf.gz | 678.6 KB | Display | |
Data in XML | 4hel_validation.xml.gz | 253.4 KB | Display | |
Data in CIF | 4hel_validation.cif.gz | 346.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/4hel ftp://data.pdbj.org/pub/pdb/validation_reports/he/4hel | HTTPS FTP |
-Related structure data
Related structure data | 1kp8S 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: 55349.285 Da / Num. of mol.: 14 / Fragment: GroEL fragment, UNP residues 2-526 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q548M1 #2: 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: 3.25 Å3/Da / Density % sol: 62.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 32% MPD, 100mM Tris-HCl, 160mM MgCl2, 10% Glycerol, 2%(w/v) PEG6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97327 Å |
Detector | Type: MARCCD225 / Detector: CCD / Date: Nov 9, 2011 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97327 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→59.4 Å / Num. all: 1247571 / Num. obs: 166588 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.32 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.4 / Num. unique all: 24106 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KP8 Resolution: 3.2→59.38 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.859 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.429 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.395 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→59.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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