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Yorodumi- PDB-5b5y: Crystal structure of PtLCIB4, a homolog of the limiting CO2-induc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b5y | ||||||
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Title | Crystal structure of PtLCIB4, a homolog of the limiting CO2-inducible protein LCIB | ||||||
Components | PtLCIB4 | ||||||
Keywords | METAL BINDING PROTEIN / metalloprotein | ||||||
Function / homology | Limiting CO2-inducible protein B/C, beta carbonyic anhydrase domain / Limiting CO2-inducible proteins B/C beta carbonyic anhydrases / metal ion binding / ACETATE ION / Limiting CO2-inducible protein B/C beta carbonyic anhydrase domain-containing protein Function and homology information | ||||||
Biological species | Phaeodactylum tricornutum (Diatom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Jin, S. / Sun, J. / Wunder, T. / Tang, D. / Mueller-Cajar, O.M. / Gao, Y. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Structural insights into the LCIB protein family reveals a new group of beta-carbonic anhydrases Authors: Jin, S. / Sun, J. / Wunder, T. / Tang, D. / Cousins, A.B. / Sze, S.K. / Mueller-Cajar, O. / Gao, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b5y.cif.gz | 111.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b5y.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 5b5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b5y_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 5b5y_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 5b5y_validation.xml.gz | 21 KB | Display | |
Data in CIF | 5b5y_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b5y ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b5y | HTTPS FTP |
-Related structure data
Related structure data | 5b5xSC 5b5zC 5b60C 5k5wC C: citing same article (ref.) 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
#1: Protein | Mass: 30482.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaeodactylum tricornutum (Diatom) / Production host: Escherichia coli (E. coli) / References: UniProt: B7FR29*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | The sequence database of this protein is BAV00141 in GenBank. The residues (-14)-1 are N-terminal ...The sequence database of this protein is BAV00141 in GenBank. The residues (-14)-1 are N-terminal expression tags. | |
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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: 2.2 Å3/Da / Density % sol: 44.19 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200 mM sodium acetate trihydrate, 100 mM Tris, 27% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.66 Å / Num. obs: 52517 / % possible obs: 93.5 % / Redundancy: 3.7 % / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.75→1.84 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B5X Resolution: 1.75→36.658 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→36.658 Å
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Refine LS restraints |
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LS refinement shell |
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