+Open data
-Basic information
Entry | Database: PDB / ID: 1i6p | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 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. GLN A 31 CA ALA A 32 N ALA A 32 CA 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. GLU A 20 GLU A 21 LYS A 28 LEU A 29 GLN A 31 ALA A 32 GLN A 33 LYS A 34 GLU A 112 GLU A 140 ARG A 141 LYS A 169 LYS A 173 ARG A 189 ARG A 198 GLU A 199 LYS A 213 LEU A 214 LYS A 215 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i6p.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i6p.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i6p_validation.pdf.gz | 364.3 KB | Display | wwPDB validaton report |
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Full document | 1i6p_full_validation.pdf.gz | 365.6 KB | Display | |
Data in XML | 1i6p_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1i6p_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/1i6p ftp://data.pdbj.org/pub/pdb/validation_reports/i6/1i6p | HTTPS FTP |
-Related structure data
Related structure data | 1i6oSC 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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Details | A tetramer constructed from the operations -y, -x, -z; y, x, -z; -1-x, 1-y, z is thought to exist in solution under physiological conditions. |
-Components
#1: Protein | Mass: 25130.779 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.009 Å3/Da / Density % sol: 36.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: ammonium sulfate, MES pH 6.3, 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: 291 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 8, 1999 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 90500 / Num. obs: 13974 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 4.4 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I6O Resolution: 2→42.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 334555.69 / 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: 44.43 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→42.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / 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: 28.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.215 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.191 |