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

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Basic information

Entry
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


2-dehydropantoate 2-reductase activity / ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / pantothenate biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Acetohydroxy acid isomeroreductase, catalytic domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Acetohydroxy acid isomeroreductase, catalytic domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
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.
History
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
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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
Polymers216,5194
Non-polymers8659
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
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.

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Components

#1: Protein
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
ChemComp-SO4 / SULFATE ION / Sulfate


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


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

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Experimental details

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Experiment

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

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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

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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

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Processing

Software
NameVersionClassification
CrystalClearv.1.3.5data reduction
AMoREphasing
CNSrefinement
CrystalClearV. 1.35 (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QMG

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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.22
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs
2.6-2.720.352713410.32140.031311836
2.72-2.860.334612860.29440.040211991
2.86-3.040.336113520.28330.052812006
3.04-3.280.308213530.2570.051211985
3.28-3.610.285413460.230.055412009
3.61-4.130.239813080.19320.046612015
4.13-5.20.20813360.16320.044812081
5.2-32.50.22813800.19920.028812157

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