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Yorodumi- PDB-3e2a: H. influenzae beta-carbonic anhydrase, variant Y181F with 100 mM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e2a | ||||||
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Title | H. influenzae beta-carbonic anhydrase, variant Y181F with 100 mM bicarbonate | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / beta carbonic anhydrase / allosteric site mutant / Metal-binding | ||||||
Function / homology | Function and homology information carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å | ||||||
Authors | Rowlett, R.S. / Lee, J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase. Authors: Rowlett, R.S. / Tu, C. / Lee, J. / Herman, A.G. / Chapnick, D.A. / Shah, S.H. / Gareiss, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e2a.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e2a.ent.gz | 207.4 KB | Display | PDB format |
PDBx/mmJSON format | 3e2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/3e2a ftp://data.pdbj.org/pub/pdb/validation_reports/e2/3e2a | HTTPS FTP |
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-Related structure data
Related structure data | 3e1vC 3e1wC 3e24C 3e28C 3e2wC 2a8dS 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: 26270.984 Da / Num. of mol.: 6 / Mutation: Y181F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: can, HI1301 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P45148, carbonic anhydrase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BCT / | #5: 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: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes, 1.5 M ammonium sulfate, 4% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 13, 2003 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.301→25 Å / Num. obs: 77406 / % possible obs: 100 % / Redundancy: 3.53 % / Rmerge(I) obs: 0.065 / Χ2: 0.999 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.301→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7649 / Χ2: 0.989 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A8D Resolution: 2.301→24.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.15 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.222 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.25 Å2 / Biso mean: 44.228 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.301→24.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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