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- PDB-3h8y: Crystal structure of carboxysome small shell protein CsoS1C from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h8y | ||||||
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Title | Crystal structure of carboxysome small shell protein CsoS1C from Halothiobacillus neapolitanus | ||||||
![]() | Major carboxysome shell protein 1C | ||||||
![]() | STRUCTURAL PROTEIN / bacterial microcompartment domain | ||||||
Function / homology | ![]() BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tsai, Y. / Sawaya, M.R. / Yeates, T.O. | ||||||
![]() | ![]() Title: Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C Authors: Tsai, Y. / Sawaya, M.R. / Yeates, T.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.6 KB | Display | ![]() |
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PDB format | ![]() | 19.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418 KB | Display | ![]() |
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Full document | ![]() | 420.3 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2g13S S: Starting model for refinement |
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Similar structure data |
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Links
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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: 9930.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: csoS1C / Plasmid: pPROEx-Htb / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris HCl pH 8.5, 0.15M Sodium Citrate, 25% PEG 400, 0.01M nickel (II) chloride, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→90 Å / Num. all: 5538 / Num. obs: 5538 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.186 / Χ2: 1.272 / Net I/σ(I): 13.17 |
Reflection shell | Resolution: 2.5→2.69 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 6.94 / Num. unique all: 1103 / Χ2: 1.18 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2G13 Resolution: 2.51→26.24 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.833 / WRfactor Rfree: 0.322 / WRfactor Rwork: 0.274 / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.554 / SU B: 14.163 / SU ML: 0.342 / SU R Cruickshank DPI: 0.37 / SU Rfree: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.3 / 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 max: 79.65 Å2 / Biso mean: 35.061 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→26.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.509→2.574 Å / Total num. of bins used: 20
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