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Yorodumi- PDB-4c3t: The Carbonic anhydrase from Thermovibrio ammonificans reveals an ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c3t | ||||||
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Title | The Carbonic anhydrase from Thermovibrio ammonificans reveals an interesting intermolecular disulfide contributing to increasing thermal stability of this enzyme | ||||||
Components | CARBONATE DEHYDRATASE | ||||||
Keywords | LYASE / THERMOPHILIC / ACETAZOLAMIDE / CARBON DIOXIDE CAPTURE / THERMAL STABILITY | ||||||
Function / homology | Function and homology information regulation of pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / zinc ion binding Similarity search - Function | ||||||
Biological species | THERMOVIBRIO AMMONIFICANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | James, P. / Isupov, M. / Sayer, C. / Berg, S. / Lioliou, M. / Kotlar, H. / Littlechild, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The Structure of a Tetrameric [Alpha]-Carbonic Anhydrase from Thermovibrio Ammonificans Reveals a Core Formed Around Intermolecular Disulfides that Contribute to its Thermostability Authors: James, P. / Isupov, M.N. / Sayer, C. / Saneei, V. / Berg, S. / Lioliou, M. / Kotlar, H. / Littlechild, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c3t.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c3t.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 4c3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c3t_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 4c3t_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 4c3t_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 4c3t_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/4c3t ftp://data.pdbj.org/pub/pdb/validation_reports/c3/4c3t | HTTPS FTP |
-Related structure data
Related structure data | 4coqC 4uovC 1kopS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 23 - 247 / Label seq-ID: 23 - 247
NCS oper: (Code: given Matrix: (-0.449, -0.524, -0.723), Vector: |
-Components
#1: Protein | Mass: 27725.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: DSMZ / Source: (natural) THERMOVIBRIO AMMONIFICANS (bacteria) / References: UniProt: E8T502, carbonic anhydrase #2: Chemical | #3: Chemical | #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: 2.28 Å3/Da / Density % sol: 46.03 % / Description: NONE |
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Crystal grow | Details: 0.5 M LICL, 50 MM SODIUM CITRATE, 10% PEG6000, PH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→80.93 Å / Num. obs: 734424 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.69→1.74 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KOP Resolution: 1.69→57.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.454 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.284 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→57.23 Å
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Refine LS restraints |
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