+Open data
-Basic information
Entry | Database: PDB / ID: 1i6o | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI BETA CARBONIC ANHYDRASE (ECCA) | ||||||
Components | CARBONIC ANHYDRASE | ||||||
Keywords | LYASE / carbonic anhydrase / metalloenzyme / zinc coordination / pH-dependent activity / MAD phasing | ||||||
Function / homology | Function and homology information carbon utilization / carbonic anhydrase / carbonate dehydratase activity / protein homotetramerization / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Cronk, J.D. / Endrizzi, J.A. / Cronk, M.R. / O'Neill, J.W. / Zhang, K.Y.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity. Authors: Cronk, J.D. / Endrizzi, J.A. / Cronk, M.R. / O'neill, J.W. / Zhang, K.Y. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Cloning, crystallization and preliminary characterization of a beta carbonic anhydrase from Escherichia coli Authors: Cronk, J.D. / O'Neill, J.W. / Cronk, M.R. / Endrizzi, J.A. / Zhang, K.Y.J. | ||||||
History |
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Remark 99 | DENSITY FOR THE FOLLOWING ATOMS WITHIN THE MAIN CHAIN IS RELATIVELY WEAK AND LIKELY REFLECTS ...DENSITY FOR THE FOLLOWING ATOMS WITHIN THE MAIN CHAIN IS RELATIVELY WEAK AND LIKELY REFLECTS INCREASED LOCAL CONFORMATIONAL FLEXIBILITY OF THE MAIN CHAIN IN THIS REGION. ALA A 32 CA GLN B 31 C GLN B 31 O ALA B 32 CA ALA B 32 O DENSITY FOR THE SIDE CHAINS OF THE LISTED RESIDUES IS RELATIVELY POORLY DEFINED. THE MODEL REPRESENTS THE MOST PROBABLE CONFORMATIONS FOR THESE RESIDUES BASED ON THE OBSERVED DENSITY. LYS A 16 GLU A 27 LYS A 28 GLN A 31 ARG A 36 GLN A 139 GLU A 140 ARG A 198 GLU A 199 LYS A 213 LEU A 214 LYS A 215 LYS B 2 LEU B 13 LYS B 16 GLU B 20 GLU B 21 LYS B 28 ARG B 36 GLU B 140 ARG B 141 LYS B 173 ARG B 206 ASN B 211 LEU B 212 LYS B 213 LEU B 214 LYS B 215 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i6o.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i6o.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i6o_validation.pdf.gz | 376.7 KB | Display | wwPDB validaton report |
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Full document | 1i6o_full_validation.pdf.gz | 381.7 KB | Display | |
Data in XML | 1i6o_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1i6o_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/1i6o ftp://data.pdbj.org/pub/pdb/validation_reports/i6/1i6o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25365.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YADF / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61517, 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: 2.64 Å3/Da / Density % sol: 51.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulfate, PEG 400, MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.3 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.96112,0.97950,0.97970,1.07812,1.28109 | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 1999 | ||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.13→45 Å / Num. all: 30857 / Num. obs: 237761 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.2 | ||||||||||||||||||
Reflection shell | Resolution: 2.13→2.25 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.255 / Num. unique all: 4186 / % possible all: 94.5 | ||||||||||||||||||
Reflection | *PLUS Num. obs: 30857 / Num. measured all: 237761 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→39.36 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2423088.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.96 Å2 / ksol: 0.3548 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→39.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.265 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.236 |