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Yorodumi- PDB-7q07: Ketol-acid reductoisomerase from Methanothermococcus thermolithot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q07 | ||||||
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Title | Ketol-acid reductoisomerase from Methanothermococcus thermolithotrophicus in the open state with NADP and tartrate | ||||||
Components | Ketol-Acid Reductoisomerase from Methanothermococcus thermolithotrophicus | ||||||
Keywords | ISOMERASE / Ketol-acid reductoisomerase / KARI / methanogenic archaea / conformational rearrangement / native purification / oligomerization / thermophile / branched-chain amino acid / biosynthesis | ||||||
Function / homology | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L(+)-TARTARIC ACID Function and homology information | ||||||
Biological species | Methanothermococcus thermolithotrophicus DSM 2095 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lemaire, O.N. / Mueller, M. / Wagner, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Biomolecules / Year: 2021 Title: Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen. Authors: Lemaire, O.N. / Muller, M.C. / Kahnt, J. / Wagner, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q07.cif.gz | 142.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q07.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 7q07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q07_validation.pdf.gz | 857.6 KB | Display | wwPDB validaton report |
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Full document | 7q07_full_validation.pdf.gz | 858 KB | Display | |
Data in XML | 7q07_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7q07_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/7q07 ftp://data.pdbj.org/pub/pdb/validation_reports/q0/7q07 | HTTPS FTP |
-Related structure data
Related structure data | 7q03SC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36556.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: / / References: ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 5 types, 146 molecules
#2: Chemical | ChemComp-TLA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-NAP / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.56 Å3/Da / Density % sol: 51.9 % / Description: Flower-shaped plates. |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: KARI was crystallized at 13.5 mg/ml in the following buffer 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% glycerol. The reservoir was filled with 90 ul crystallization solution (33 % (w/v) ...Details: KARI was crystallized at 13.5 mg/ml in the following buffer 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% glycerol. The reservoir was filled with 90 ul crystallization solution (33 % (w/v) PEG 5000 MME, 100 mM MES/NaOH pH 6.5 and 200 mM ammonium sulphate). Drops of 0.7 ul protein with 0.7 ul of crystallisation solution were applied on the shelf. Crystals were firstly soaked in the crystallisation solution supplemented with 20 mM NADP, 50 mM L-Tartrate and 50 mM MgCl2 for 3 minutes, and then soaked in the crystallisation solution supplemented with 30 % v/v glycerol before freezing. Temp details: +/- 3 degree |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection twin | Operator: -l,-k,-h / Fraction: 0.12 |
Reflection | Resolution: 2.2→46.25 Å / Num. obs: 19073 / % possible obs: 100 % / Redundancy: 18.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.039 / Rrim(I) all: 0.168 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2766 / CC1/2: 0.385 / Rpim(I) all: 0.166 / Rrim(I) all: 0.554 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Q03 Resolution: 2.2→41.37 Å / Cross valid method: THROUGHOUT / σ(F): 133.59 / Phase error: 21.21 / Stereochemistry target values: TWIN_LSQ_F Details: The refinement was performed with TLS and intensity-based twin refinement with the following twin law -l,-k,-h
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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 max: 98.42 Å2 / Biso mean: 30.3423 Å2 / Biso min: 9.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→41.37 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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