+Open data
-Basic information
Entry | Database: PDB / ID: 4lj4 | ||||||
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Title | ClpB NBD2 from T. thermophilus, nucleotide-free | ||||||
Components | Chaperone protein ClpB | ||||||
Keywords | CHAPERONE / AAA+ protein / nucleotide binding domain / molecular chaperone / disaggregase | ||||||
Function / homology | Function and homology information protein unfolding / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å | ||||||
Authors | Zeymer, C. / Barends, T.R.M. / Werbeck, N.D. / Schlichting, I. / Reinstein, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor Authors: Zeymer, C. / Barends, T.R.M. / Werbeck, N.D. / Schlichting, I. / Reinstein, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lj4.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lj4.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 4lj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lj4_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 4lj4_full_validation.pdf.gz | 443.4 KB | Display | |
Data in XML | 4lj4_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4lj4_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/4lj4 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/4lj4 | HTTPS FTP |
-Related structure data
Related structure data | 4lj5C 4lj6C 4lj7C 4lj8C 4lj9C 4ljaC 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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Details | THE FULL PROTEIN FORMS A RANGE OF OLIGOMERS, AND THIS DOMAIN FORMS DIMERS IN SOLUTION UNDER CERTAIN CIRCUMSTANCES. |
-Components
#1: Protein | Mass: 38358.000 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain 2, UNP residues 520-854 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: clpB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9RA63 |
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#2: Chemical | ChemComp-PO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M sodium citrate, 0.1M HEPES/NaOH, 20% isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9495 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2005 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9495 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 9176 / Num. obs: 9176 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.8→3 Å / Rmerge(I) obs: 0.534 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→19.68 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.851 / SU B: 35.56 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R: 1.102 / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.341 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.68 Å
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