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Yorodumi- PDB-4i61: Crystal structure of a trimeric bacterial microcompartment shell ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i61 | ||||||
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Title | Crystal structure of a trimeric bacterial microcompartment shell protein PduB | ||||||
Components | Propanediol utilization protein PduB | ||||||
Keywords | STRUCTURAL PROTEIN / BMC Domain / Shell Protein | ||||||
Function / homology | Bacterial microcompartment shell protein PduB / Bacterial microcompartment shell protein, EutL/PduB type / bacterial microcompartment / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / structural molecule activity / Propanediol utilization protein PduB Function and homology information | ||||||
Biological species | Lactobacillus reuteri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Pang, A.H. / Pickersgill, R.W. | ||||||
Citation | Journal: To be Published Title: Propionaldehyde does not bind to PduB Authors: Pang, A.H. / 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 | 4i61.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i61.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 4i61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i61 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i61 | HTTPS FTP |
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-Related structure data
Related structure data | 4fayS 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 on special symmetry positions |
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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: ATCC 55730 / SD2112 / Gene: HMPREF0538_20934, pduB / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F8DQ39 #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: 1.87 Å3/Da / Density % sol: 34.19 % |
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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 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2012 |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→59.77 Å / Num. obs: 74480 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 9.6 / Redundancy: 4.9 % / Biso Wilson estimate: 9.916 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.074 / Net I/σ(I): 0.102 |
Reflection shell | Resolution: 1.64→1.68 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.2 / Num. unique all: 26795 / Rsym value: 0.393 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FAY Resolution: 1.64→59.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.925 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.097 / 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: 11.795 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→59.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.683 Å / Total num. of bins used: 20
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