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- PDB-1yrl: Escherichia coli ketol-acid reductoisomerase -

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Basic information

Database: PDB / ID: 1yrl
TitleEscherichia coli ketol-acid reductoisomerase
ComponentsKetol-acid reductoisomerase
KeywordsOXIDOREDUCTASE / Branched-chain amino acid biosynthesis / knotted protein / reductoisomerase
Function / homology
Function and homology information

ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / branched-chain amino acid biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / NADP binding / protein homotetramerization / magnesium ion binding / identical protein binding / cytosol
Ketol-acid reductoisomerase, C-terminal / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / KARI C-terminal domain profile. / KARI N-terminal domain profile. / Acetohydroxy acid isomeroreductase, NADPH-binding domain / Acetohydroxy acid isomeroreductase, catalytic domain / NAD(P)-binding domain superfamily / 6-phosphogluconate dehydrogenase, domain 2 / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase
Ketol-acid reductoisomerase (NADP(+))
Biological speciesEscherichia coli (E. coli)
AuthorsTyagi, R. / Duquerroy, S. / Navaza, J. / Guddat, L.W. / Duggleby, R.G.
CitationJournal: Protein Sci. / Year: 2005
Title: The crystal structure of a bacterial class II ketol-acid reductoisomerase: domain conservation and evolution
Authors: Tyagi, R. / Duquerroy, S. / Navaza, J. / Guddat, L.W. / Duggleby, R.G.
Validation Report
SummaryFull reportAbout validation report
DepositionFeb 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

Structure visualization

Structure viewerMolecule:

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Deposited unit
A: Ketol-acid reductoisomerase
B: Ketol-acid reductoisomerase
C: Ketol-acid reductoisomerase
D: Ketol-acid reductoisomerase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)217,38413

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)226.882, 226.882, 118.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe tetramer can be assembled by combination of the A and D chains with the B and C chains generated by the symmetry operator 1-Y,1+X-Y,Z.


#1: Protein/peptide
Ketol-acid reductoisomerase / / Acetohydroxy-acid isomeroreductase / Alpha-keto-beta-hydroxylacil reductoisomerase

Mass: 54129.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ilvC / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P05793, ketol-acid reductoisomerase (NADP+)
#2: Chemical

Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O / Water

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, sodium bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 26, 2003 / Details: mirrors
RadiationMonochromator: double focussed mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→32.48 Å / Num. all: 106858 / Num. obs: 106858 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 20.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.1 / Num. unique all: 10653 / Rsym value: 0.3 / % possible all: 98.5


CrystalClearv.1.3.5data reduction
CrystalClearV. 1.35 (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QMG
Resolution: 2.6→32.48 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 10702 -Random
Rwork0.223 ---
All0.227 106782 --
Obs0.227 106858 99.8 %-
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.538 Å2-6.854 Å20 Å2
2--3.538 Å20 Å2
3----7.077 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14443 0 45 416 14904
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.22
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs

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