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Open data
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Basic information
Entry | Database: PDB / ID: 4lj5 | ||||||
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Title | ClpB NBD2 from T. thermophilus in complex with ADP | ||||||
![]() | 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 | ![]() | 139.8 KB | Display | ![]() |
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PDB format | ![]() | 109.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 795.1 KB | Display | ![]() |
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Full document | ![]() | 796.2 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lj4C ![]() 4lj6C ![]() 4lj7C ![]() 4lj8C ![]() 4lj9C ![]() 4ljaC ![]() 1qvrS 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-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
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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, 2mM ADP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2003 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01096 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 17302 / Num. obs: 17302 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.12 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2.12 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QVR Resolution: 2.4→19.27 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 19.264 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.466 / ESU R Free: 0.283 / 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: 65.332 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 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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