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Yorodumi- PDB-7lat: Campylobacter jejuni keto-acid reductoisomerase in complex with Mg2+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lat | ||||||
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Title | Campylobacter jejuni keto-acid reductoisomerase in complex with Mg2+ | ||||||
Components | Ketol-acid reductoisomerase | ||||||
Keywords | ISOMERASE / metalloenzyme / reductoisomerase | ||||||
Function / homology | Function and homology information ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process / isomerase activity / NADP binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | ||||||
Authors | Guddat, L.W. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Acs Catalysis / Year: 2024 Title: Mapping of the Reaction Trajectory catalyzed by Class I Ketol-Acid Reductoisomerase Authors: Lin, X. / Lonhienne, T. / Lv, Y. / Kurz, J. / McGeary, R. / Schenk, G. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lat.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lat.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lat_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7lat_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7lat_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7lat_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/7lat ftp://data.pdbj.org/pub/pdb/validation_reports/la/7lat | HTTPS FTP |
-Related structure data
Related structure data | 8swmC 8sxdC 8upnC 8uppC 8upqC 4ypoS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35868.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ilvC, CW563_00670 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5T0UG45 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Ppt buffer 0.2 M Li2SO4, 0.1 M Bis-Tris pH 5.5, 20% PEG3350. The well solution (which was not added to the drop) 35% PEG3350, 250 mM MgCl2, 20 mM Tris-HCl pH 8.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 1, 2016 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→45.52 Å / Num. obs: 12844 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.5 % / Biso Wilson estimate: 37.3319105008 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.027 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.47→2.59 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1441 / Rpim(I) all: 0.178 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YPO Resolution: 2.47→45.52 Å / SU ML: 0.26725473031 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4152515085
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3898217922 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→45.52 Å
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Refine LS restraints |
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LS refinement shell |
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