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- PDB-7bnh: Complex structure at atomic resolution of SH3b domain with benzoi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bnh | ||||||
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Title | Complex structure at atomic resolution of SH3b domain with benzoic acid | ||||||
![]() | Lysostaphin | ||||||
![]() | CELL ADHESION / CELL WALL TARGETING/BINDING / CWT / SH3 / COMPLEX / BENZOIC ACID / Staphylococcus simulans | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malecki, P.H. / Sabala, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Complex structure of SH3b domain with benzoic acid Authors: Malecki, P.H. / Sabala, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.7 KB | Display | ![]() |
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PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 693.5 KB | Display | ![]() |
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Full document | ![]() | 693.6 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5leoS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10819.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 462 molecules ![](data/chem/img/BEZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-BEZ / | ||||||
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#3: Chemical | ChemComp-GOL / | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-MES / | #7: 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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 6.5 Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% PEG 5K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.84→37.501 Å / Num. obs: 141746 / % possible obs: 83.7 % / Redundancy: 3.776 % / Biso Wilson estimate: 6.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.032 / Χ2: 0.954 / Net I/σ(I): 27.6 / Num. measured all: 535196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LEO Resolution: 0.84→17.21 Å / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 9.24 / 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: 126.17 Å2 / Biso mean: 13.8033 Å2 / Biso min: 0.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.84→17.21 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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