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- PDB-1qmg: Acetohydroxyacid isomeroreductase complexed with its reaction pro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qmg | ||||||
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Title | Acetohydroxyacid isomeroreductase complexed with its reaction product dihydroxy-methylvalerate, manganese and ADP-ribose. | ||||||
![]() | ACETOHYDROXY-ACID ISOMEROREDUCTASE | ||||||
![]() | OXIDOREDUCTASE / BRANCHED CHAIN AMINO ACID BIOSYNTHESIS / REACTION PRODUCT / MANGANESE / ADP-RIBOSE | ||||||
Function / homology | ![]() ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / NADPH binding / amino acid biosynthetic process / chloroplast / magnesium ion binding / protein homodimerization activity / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomazeau, K. / Dumas, R. / Halgand, F. / Douce, R. / Biou, V. | ||||||
![]() | ![]() Title: Structure of Spinach Acetohydroxyacid Isomeroreductase Complexed with its Product of Reaction Dihydroxy-Methylvalerate, Manganese and Adp-Ribose Authors: Thomazeau, K. / Dumas, R. / Halgand, F. / Forest, E. / Douce, R. / Biou, V. #1: ![]() Title: The Crystal Structure of Plant Acetohydroxyacid Isomeroreductase Complexed with its Reaction Product Dihydroxymethylvalerate, Manganese and (Phospho)-Adp-Ribose Authors: Biou, V. / Dumas, R. / Cohen-Addad, C. / Douce, R. / Job, D. / Pebay-Peyroula, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 442.9 KB | Display | ![]() |
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PDB format | ![]() | 360.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 93.3 KB | Display | |
Data in CIF | ![]() | 141.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yveS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 57045.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene (production host): CDNA FROM ACETOHYDROXY ACID ISOMEROREDUCTASE Production host: ![]() ![]() References: UniProt: Q01292, ketol-acid reductoisomerase (NADP+) |
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-Non-polymers , 5 types, 2106 molecules ![](data/chem/img/APX.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMV.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-APX / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-DMV / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE MATURE AMINO ACID SEQUENCE IS DEVOID OF SIGNAL PEPTIDE. THEREFORE, RESIDUE 72 IS THE N-TERMINAL ...THE MATURE AMINO ACID SEQUENCE IS DEVOID OF SIGNAL PEPTIDE. THEREFORE, RESIDUE 72 IS THE N-TERMINAL AMINO ACID. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 Details: PROTEIN WAS CRYSTALLISED FROM 1.8 M AMMONIUM SULFATE IN 0.1 M TRIS-HCL AT PH 7.2 IN THE PRESENCE OF AHB, NADPH, AND MN2+. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Dumas, R., (1994) J. Mol. Biol., 242, 578. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1996 / Details: 2 MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26 Å / Num. obs: 299230 / % possible obs: 96.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.054 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 14.6 / Rsym value: 0.096 / % possible all: 96.6 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.096 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YVE Resolution: 1.6→10 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2603215.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: NCS RESTRAINTS HAVE BEEN APPLIED UNTIL THE R-FACTOR DROPPED TO A VALUE OF 0.200. THEN THEY WERE PROGRESSIVELY LOOSENED AND REMOVED BECAUSE THE RATIO BETWEEN THE NUMBER OF REFLECTIONS AND ...Details: NCS RESTRAINTS HAVE BEEN APPLIED UNTIL THE R-FACTOR DROPPED TO A VALUE OF 0.200. THEN THEY WERE PROGRESSIVELY LOOSENED AND REMOVED BECAUSE THE RATIO BETWEEN THE NUMBER OF REFLECTIONS AND NUMBER OF DEGREES OF FREEDOM MADE IT POSSIBLE.
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Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.193 / Rfactor Rfree: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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