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Yorodumi- PDB-5jj8: Crystal Structure of the Beta Carbonic Anhydrase psCA3 isolated f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jj8 | ||||||
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Title | Crystal Structure of the Beta Carbonic Anhydrase psCA3 isolated from Pseudomonas aeruginosa - alternate crystal packing form | ||||||
Components | Carbonic anhydrase | ||||||
Keywords | LYASE / psCA3 / crystal packing / beta-carbonic anhydrase | ||||||
Function / homology | Function and homology information carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.585 Å | ||||||
Authors | Pinard, M.A. / Kurian, J.J. / Aggarwal, M. / Agbandje-McKenna, M. / McKenna, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Cryoannealing-induced space-group transition of crystals of the carbonic anhydrase psCA3. Authors: Pinard, M.A. / Kurian, J.J. / Aggarwal, M. / Agbandje-McKenna, M. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jj8.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jj8.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/5jj8 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/5jj8 | HTTPS FTP |
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-Related structure data
Related structure data | 4rxyS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24250.568 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: can_1, can, yadF, AO943_21535, AO946_10560, AOD73_25440, AOU28_24465, AOY09_00950, APT60_24635, ATC05_14980, AU380_02155, ERS445055_04974, HV95_21180, HV96_01220, HV97_23895, HV98_01810, HV99_ ...Gene: can_1, can, yadF, AO943_21535, AO946_10560, AOD73_25440, AOU28_24465, AOY09_00950, APT60_24635, ATC05_14980, AU380_02155, ERS445055_04974, HV95_21180, HV96_01220, HV97_23895, HV98_01810, HV99_02890, HW00_06825, HW01_20790, HW02_08065, HW03_11820, HW04_25045, HW05_22660, HW06_00905, HW07_08265, HW08_30020, HW09_16360, HW10_17975, IOMTU133_5488, PA257_5879, PA8380_53220, PAERUG_E15_London_28_01_14_01862, PAERUG_P32_London_17_VIM_2_10_11_05532, PAO1OR4768 Production host: Escherichia coli (E. coli) References: UniProt: A0A072ZBL6, UniProt: Q9HVB9*PLUS, carbonic anhydrase #2: Chemical | #3: 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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: Hampton Research Crystal Screen 2, PEG/Ion, PEG/Ion 2, an in-house sodium citrate screen (screening conditions varied from 1.1 to 1.8 M sodium citrate, Tris-HCl pH 7.1-8.1), and an in-house ...Details: Hampton Research Crystal Screen 2, PEG/Ion, PEG/Ion 2, an in-house sodium citrate screen (screening conditions varied from 1.1 to 1.8 M sodium citrate, Tris-HCl pH 7.1-8.1), and an in-house ammonium sulfate screen (screening conditions varied from 1.8 M to 2.8 M ammonium sulfate, 0.1 M malic acid, 0.1 M imidazole pH 7.0-8.5) prepared by the Rigaku Alchemist DT were used to screen for optimum crystallization conditions. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9177 Å / Relative weight: 1 |
Reflection | Resolution: 2.585→35.553 Å / Num. obs: 14191 / % possible obs: 91.48 % / Redundancy: 3.2 % / Net I/σ(I): 17.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RXY Resolution: 2.585→35.553 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.585→35.553 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.6609 Å / Origin y: -9.0053 Å / Origin z: -16.6188 Å
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Refinement TLS group | Selection details: all |