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Open data
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Basic information
Entry | Database: PDB / ID: 4lj6 | ||||||
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Title | ClpB NBD2 from T. thermophilus in complex with AMPPCP | ||||||
![]() | Chaperone protein ClpB | ||||||
![]() | CHAPERONE / AAA+ protein / nucleotide binding domain / molecular chaperone / disaggregase | ||||||
Function / homology | ![]() protein unfolding / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeymer, C. / Barends, T.R.M. / Werbeck, N.D. / Schlichting, I. / Reinstein, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.6 KB | Display | ![]() |
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PDB format | ![]() | 109.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 766 KB | Display | ![]() |
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Full document | ![]() | 767.7 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lj4C ![]() 4lj5SC ![]() 4lj7C ![]() 4lj8C ![]() 4lj9C ![]() 4ljaC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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. |
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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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ACP / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % |
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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, 2mM AMPPCP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 7, 2006 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 28958 / Num. obs: 28959 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4115 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LJ5 Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.985 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.161 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.589 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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