+Open data
-Basic information
Entry | Database: PDB / ID: 8b3s | ||||||
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Title | Structure of YjbA in complex with ClpC N-terminal Domain | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / sporulation | ||||||
Function / homology | Function and homology information peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Evans, N.J. / Isaacson, R.L. / Camp, A.H. / Collins, M.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure of YjbA in complex with ClpC N-terminal Domain Authors: Evans, N.J. / Isaacson, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b3s.cif.gz | 189 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b3s.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 8b3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/8b3s ftp://data.pdbj.org/pub/pdb/validation_reports/b3/8b3s | HTTPS FTP |
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-Related structure data
Related structure data | 5hbnS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42370.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) Gene: B4122_0676, B4417_4067, Bateq7PJ16_1268, DFO69_2911, J5227_16610, SC09_Contig19orf00439, yjbA, BSU11410 Strain: 168 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085CA92, UniProt: O31597 | ||||||
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#2: Protein | Mass: 16947.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_1475 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164W157 | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.96 % / Description: Rods |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4% PEG 8000, 0.2 M Magnesium Chloride / Temp details: bench top incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→29.9 Å / Num. obs: 28876 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 1 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.09→2.13 Å / Redundancy: 8.8 % / Num. unique obs: 1440 / CC1/2: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5hbn Resolution: 2.09→29.867 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.11 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→29.867 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.0773 Å / Origin y: -0.9208 Å / Origin z: 2.6425 Å
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Refinement TLS group | Selection details: all |