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Yorodumi- PDB-3tio: Crystal structures of yrdA from Escherichia coli, a homologous pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tio | ||||||
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Title | Crystal structures of yrdA from Escherichia coli, a homologous protein of gamma-class carbonic anhydrase, show possible allosteric conformations | ||||||
Components | Protein YrdA | ||||||
Keywords | TRANSFERASE / Carbonic anhydrase (CA) catalyzes / zinc ion binding | ||||||
Function / homology | Function and homology information protein-containing complex / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | ||||||
Authors | Park, H.M. / Choi, J.W. / Lee, J.E. / Jung, C.H. / Kim, B.Y. / Kim, J.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structures of the gamma-class carbonic anhydrase homologue YrdA suggest a possible allosteric switch Authors: Park, H.M. / Park, J.H. / Choi, J.W. / Lee, J.E. / Kim, B.Y. / Jung, C.H. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tio.cif.gz | 238.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tio.ent.gz | 189.1 KB | Display | PDB format |
PDBx/mmJSON format | 3tio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tio_validation.pdf.gz | 483.2 KB | Display | wwPDB validaton report |
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Full document | 3tio_full_validation.pdf.gz | 497.8 KB | Display | |
Data in XML | 3tio_validation.xml.gz | 53.2 KB | Display | |
Data in CIF | 3tio_validation.cif.gz | 76.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/3tio ftp://data.pdbj.org/pub/pdb/validation_reports/ti/3tio | HTTPS FTP |
-Related structure data
Related structure data | 3tisC 1v3wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20116.754 Da / Num. of mol.: 6 / Mutation: R6H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yrdA, b3279, JW5710 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9W9 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PO4 / #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: 1.91 Å3/Da / Density % sol: 35.6 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 4.6 Details: 20 % (w/v) polyethyleneglycol Monomethyl Ether 2000, 0.15M (NH4)2SO4, 0.1M Sodium Acetate, pH 4.6, EVAPORATION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→50 Å / Num. obs: 173327 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.41→1.43 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V3W Resolution: 1.41→50 Å / σ(F): -3
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Refinement step | Cycle: LAST / Resolution: 1.41→50 Å
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Refine LS restraints |
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