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Yorodumi- PDB-4xdz: Holo structure of ketol-acid reductoisomerase from Ignisphaera ag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xdz | ||||||
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Title | Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans | ||||||
Components | Ketol-acid reductoisomerase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information ketol-acid reductoisomerase [NAD(P)+] / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Ignisphaera aggregans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Cahn, J.K.B. / Brinkmann-Chen, S. / Arnold, F.H. | ||||||
Citation | Journal: Biochem.J. / Year: 2015 Title: Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases. Authors: Cahn, J.K. / Brinkmann-Chen, S. / Spatzal, T. / Wiig, J.A. / Buller, A.R. / Einsle, O. / Hu, Y. / Ribbe, M.W. / Arnold, F.H. #1: Journal: Metab. Eng. / Year: 2014 Title: Uncovering rare NADH-preferring ketol-acid reductoisomerases. Authors: Brinkmann-Chen, S. / Cahn, J.K. / Arnold, F.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xdz.cif.gz | 304.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xdz.ent.gz | 246 KB | Display | PDB format |
PDBx/mmJSON format | 4xdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xdz_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4xdz_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4xdz_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 4xdz_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/4xdz ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xdz | HTTPS FTP |
-Related structure data
Related structure data | 4xdyC 4xehC 4xiyC 4kqxS 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 | biological unit is the same as asym. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38465.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ignisphaera aggregans (archaea) / Strain: DSM 17230 / JCM 13409 / AQ1.S1 / Gene: ilvC, Igag_1561 / Plasmid: pET22b(+) / Production host: Escherichia Coli (E. coli) / Strain (production host): BL-21 (DE3) References: UniProt: E0SRA9, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 6 types, 610 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: 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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M bis-tris pH 6, 22% polyethylene glycol monomethylether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→68.415 Å / Num. obs: 236179 / % possible obs: 95 % / Redundancy: 3 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.096 / Rsym value: 0.079 / Net I/av σ(I): 5.195 / Net I/σ(I): 6.9 / Num. measured all: 662948 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KQX Resolution: 1.15→68.415 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1737 / WRfactor Rwork: 0.1413 / FOM work R set: 0.7951 / SU B: 1.683 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0363 / SU Rfree: 0.0379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.77 Å2 / Biso mean: 13.086 Å2 / Biso min: 5.42 Å2
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Refinement step | Cycle: final / Resolution: 1.15→68.415 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.178 Å / Total num. of bins used: 20
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