+Open data
-Basic information
Entry | Database: PDB / ID: 7dsg | ||||||
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Title | Crystal structure of Brucella abortus PhiA | ||||||
Components | Brucella Abortus PhiA | ||||||
Keywords | UNKNOWN FUNCTION / T4SS / lysozyme inhibitor / PliC | ||||||
Function / homology | C-type lysozyme inhibitor superfamily / MliC domain-containing protein Function and homology information | ||||||
Biological species | Brucella abortus biovar 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hyun, Y. / Ha, N.-C. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Brucella abortus PhiA Authors: Hyun, Y. / Ha, N.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dsg.cif.gz | 34.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dsg.ent.gz | 18.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/7dsg ftp://data.pdbj.org/pub/pdb/validation_reports/ds/7dsg | HTTPS FTP |
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-Related structure data
Related structure data | 4mirS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12199.530 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus biovar 1 (strain 9-941) (bacteria) Strain: 9-941 / Gene: BruAb1_0102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57FR6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop Details: 2% Tacsimate pH 6.5, 0.1 M BIS-TRIS pH 6.5, 24% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 298.15 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: May 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.95 Å / Num. obs: 17157 / % possible obs: 100 % / Redundancy: 108.3 % / Biso Wilson estimate: 38.63 Å2 / CC star: 0.99 / R split: 0.1716 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique obs: 5214 / CC star: 0.92 / R split: 0.7431 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MIR Resolution: 1.9→45.94 Å / SU ML: 0.2668 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9499 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 45.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.94 Å
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Refine LS restraints |
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LS refinement shell |
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