+Open data
-Basic information
Entry | Database: PDB / ID: 7dpy | ||||||
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Title | 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 bv. 1 str. 9-941 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hyun, Y. / Ha, N.-C. | ||||||
Citation | Journal: Mol.Cells / Year: 2021 Title: Structure and Function of the Autolysin SagA in the Type IV Secretion System of Brucella abortus . Authors: Hyun, Y. / Baek, Y. / Lee, C. / Ki, N. / Ahn, J. / Ryu, S. / 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 | 7dpy.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dpy.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 7dpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/7dpy ftp://data.pdbj.org/pub/pdb/validation_reports/dp/7dpy | HTTPS FTP |
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-Related structure data
Related structure data | 7dnpC 4mirS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 12267.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal sequence was confirmed by Edman degradation sequencing method. 101-108 residues are expression tag sequence, for both chain A and B. Source: (gene. exp.) Brucella abortus bv. 1 str. 9-941 (bacteria) Strain: 9-941 / Gene: BruAb1_0102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57FR6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BIS-TRIS pH 6.0, 18% (w/v) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 19949 / % possible obs: 99 % / Redundancy: 9.7 % / Biso Wilson estimate: 17.16 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.311 / Num. unique obs: 964 / CC1/2: 0.953 / CC star: 0.988 / Rpim(I) all: 0.097 / Rrim(I) all: 0.276 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MIR Resolution: 1.8→45.36 Å / SU ML: 0.1729 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 21.487 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: 19.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.36 Å
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Refine LS restraints |
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LS refinement shell |
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