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Yorodumi- PDB-4mir: The structure of Brucella abortus PliC in the hexagonal crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mir | ||||||
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Title | The structure of Brucella abortus PliC in the hexagonal crystal form | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | HYDROLASE INHIBITOR / lysozyme | ||||||
Function / homology | C-type lysozyme inhibitor / Membrane-bound lysozyme-inhibitor of c-type lysozyme / C-type lysozyme inhibitor / C-type lysozyme inhibitor superfamily / Lipocalin / Beta Barrel / Mainly Beta / membrane / C-type lysozyme inhibitor domain-containing protein Function and homology information | ||||||
Biological species | Brucella abortus bv. 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ha, N.C. / Um, S.H. / Kim, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural basis for the inhibition of human lysozyme by PliC from Brucella abortus Authors: Um, S.H. / Kim, J.S. / Kim, K. / Kim, N. / Cho, H.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 | 4mir.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mir.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/4mir ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mir | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10646.972 Da / Num. of mol.: 3 / Fragment: UNP residues 27-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus bv. 1 (bacteria) / Strain: 9-941 / Gene: BruAb1_0462 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57ES7 #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: 2.81 Å3/Da / Density % sol: 56.23 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate, 2.0M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 5, 2012 | |||||||||||||||||||||
Radiation | Monochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.4→20 Å / Num. all: 15664 / Num. obs: 15422 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.752 Å / SU ML: 0.35 / σ(F): 1.52 / Phase error: 22.73 / 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: 2.4→19.752 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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