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Yorodumi- PDB-2flz: The X-ray structure of cis-3-chloroacrylic acid dehalogenase (cis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2flz | ||||||
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Title | The X-ray structure of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) with a sulfate ion bound in the active site | ||||||
Components | cis-3-chloroacrylic acid dehalogenase | ||||||
Keywords | HYDROLASE / 3-chloroacrylic acid dehalogenase / 4OT / hydratase / dehalogenation / 4-oxalocrotonate tautomerase | ||||||
Function / homology | Tautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / : / Cis-3-chloroacrylic acid dehalogenase Function and homology information | ||||||
Biological species | coryneform bacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | de Jong, R.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structures of Native and Inactivated cis-3-Chloroacrylic Acid Dehalogenase: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY AND INACTIVATION BY (R)-OXIRANE-2-CARBOXYLATE. Authors: de Jong, R.M. / Bazzacco, P. / Poelarends, G.J. / Johnson, W.H. / Kim, Y.J. / Burks, E.A. / Serrano, H. / Thunnissen, A.-M.W.H. / Whitman, C.P. / Dijkstra, B.W. | ||||||
History |
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Remark 999 | SEQUENCE THE AUTHOR MAINTAINS THAT THIS IS AN ERROR IN THE SEQUENCE DATABASE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2flz.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2flz.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 2flz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2flz_validation.pdf.gz | 463.3 KB | Display | wwPDB validaton report |
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Full document | 2flz_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 2flz_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 2flz_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/2flz ftp://data.pdbj.org/pub/pdb/validation_reports/fl/2flz | HTTPS FTP |
-Related structure data
Related structure data | 2fltC 1fltS 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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2 |
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3 |
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Unit cell |
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Details | The biological unit is a trimer. The ASU contains three monomers, which form three trimers by rotation around the crystallographic three-fold symmetry axis |
-Components
#1: Protein | Mass: 16630.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) coryneform bacterium (bacteria) / Plasmid: pBAD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: GenBank: 37702690, UniProt: Q6VPE5*PLUS, Hydrolases; Acting on halide bonds; In carbon-halide compounds #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: 4.66 Å3/Da / Density % sol: 73.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: equal amounts of protein solution (10 mg/mL) and well solution containing 10% (v/v) 2-propanol as a precipitant, 100 mM phosphate-citrate buffer, pH 4.2, and 0.2 M Li2SO4, VAPOR DIFFUSION, ...Details: equal amounts of protein solution (10 mg/mL) and well solution containing 10% (v/v) 2-propanol as a precipitant, 100 mM phosphate-citrate buffer, pH 4.2, and 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. all: 24413 / Num. obs: 24413 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 90 Å2 / Rsym value: 0.093 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.75→2.87 Å / Mean I/σ(I) obs: 3.5 / Num. unique all: 1222 / Rsym value: 0.359 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: cis-3-chloroacrylic acid dehalogenase inactivated (1FLT) Resolution: 2.75→39.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3763590.05 / Data cutoff high rms absF: 3763590.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.9622 Å2 / ksol: 0.328788 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→39.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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