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Open data
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Basic information
Entry | Database: PDB / ID: 7n46 | ||||||
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Title | ADP-binding state of the nucleotide-binding domain of Hsp70 DnaK | ||||||
![]() | Chaperone protein DnaK | ||||||
![]() | CHAPERONE / molecular chaperone / Hsp70 / protein folding | ||||||
Function / homology | ![]() unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, W. / Hendrickson, W.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational equilibria in allosteric control of Hsp70 chaperones. Authors: Wang, W. / Liu, Q. / Liu, Q. / Hendrickson, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.7 KB | Display | ![]() |
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PDB format | ![]() | 127.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ko2C ![]() 7krtC ![]() 7kruC ![]() 7krvC ![]() 7krwC ![]() 7raxC ![]() 1bupS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41783.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: dnaK, FAZ83_07380 Production host: ![]() ![]() References: UniProt: A0A6D2W465 |
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-Non-polymers , 5 types, 200 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / |
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#3: Chemical | ChemComp-NO3 / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-PO4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.08 % |
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Crystal grow | Temperature: 277.15 K / Method: evaporation Details: 0.04 M HEPES pH 7.5, 20% PEG 3350, 0.1 M magnesium nitrate, 0.02 M sodium chloride, 0.01 M phosphate-citrate pH 4.2, 1% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.21→48.25 Å / Num. obs: 24196 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.96 / Rmerge(I) obs: 0.625 / Rpim(I) all: 0.199 / Rrim(I) all: 0.657 / Net I/σ(I): 3.7 / Num. measured all: 256415 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BUP Resolution: 2.21→48.25 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.97 Å2 / Biso mean: 30.1686 Å2 / Biso min: 13.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.21→48.25 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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