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- PDB-3e3f: H. influenzae beta-carbonic anhydrase, variant V47A with 100 mM b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3e3f | ||||||
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Title | H. influenzae beta-carbonic anhydrase, variant V47A with 100 mM bicarbonate | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE / beta carbonic anhydrase / allosteric site mutant / Metal-binding | ||||||
Function / homology | ![]() carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rowlett, R.S. / Mysliwiec, M. | ||||||
![]() | ![]() Title: Evidence for a bicarbonate "escort" site in Haemophilus influenzae beta-carbonic anhydrase . Authors: Rowlett, R.S. / Hoffmann, K.M. / Failing, H. / Mysliwiec, M.M. / Samardzic, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 65.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3e2xC ![]() 3e31C ![]() 3e3gC ![]() 3e3iC ![]() 2a8dS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 26258.932 Da / Num. of mol.: 2 / Mutation: V47A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-BCT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 0.7 M sodium potassium tartrate, 100 mM sodium bicarbonate, 12 mg/mL protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→76.472 Å / Num. obs: 30001 / % possible obs: 99.2 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / Num. measured all: 16260 / Num. unique all: 4077 / Rsym value: 0.367 / % possible all: 94.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2A8D Resolution: 2.3→28.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.754 / SU B: 16.172 / SU ML: 0.186 / SU R Cruickshank DPI: 0.195 / SU Rfree: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.176 / 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: 86.61 Å2 / Biso mean: 48.922 Å2 / Biso min: 22.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→28.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→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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