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Yorodumi- PDB-4fay: Crystal structure of a trimeric bacterial microcompartment shell ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fay | ||||||
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Title | Crystal structure of a trimeric bacterial microcompartment shell protein PduB with glycerol metabolites | ||||||
Components | Microcompartments proteinBacterial microcompartment | ||||||
Keywords | glycerol-binding protein / BMC Domain / Shell Protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus reuteri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Pang, A.H. / Prentice, M.B. / Pickersgill, R.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB. Authors: Pang, A. / Liang, M. / Prentice, M.B. / Pickersgill, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fay.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fay.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/4fay ftp://data.pdbj.org/pub/pdb/validation_reports/fa/4fay | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27051.662 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: DSM 20016 / Gene: Lreu_1748, PduB / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5VMB3 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACT / | #4: 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: 1.89 Å3/Da / Density % sol: 35.02 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate, 1.4 M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2012 |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→72.78 Å / Num. obs: 87436 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2 / Num. unique all: 12243 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EtuB Resolution: 1.56→72.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.043 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.515 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→72.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.555→1.596 Å / Total num. of bins used: 20
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