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- PDB-6l2r: IlvC, a ketol-acid reductoisomerase, from Streptococcus pneumonia... -

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Basic information

Entry
Database: PDB / ID: 6l2r
TitleIlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_E195S
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsISOMERASE / IlvC / Stereptococcus pneumoniae / BCAA pathway / ketol-acid reductoisomerase / E195S
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGyuhee, K. / Donghyuk, S. / Sumin, L. / Jaesook, Y. / Sangho, L.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01367602 Korea, Republic Of
National Research Foundation (Korea)NRF-2018R1A2B6004367 Korea, Republic Of
National Research Foundation (Korea)NRF-2019R1A6A7076041 Korea, Republic Of
National Research Foundation (Korea)SRC-2017R1A5A1014560 Korea, Republic Of
CitationJournal: Crystals / Year: 2019
Title: Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae.
Authors: Kim, G.H. / Shin, D.H. / Lee, S.M. / Yoon, J.S. / Lee, S.H.
History
DepositionOct 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase (NADP(+))
B: Ketol-acid reductoisomerase (NADP(+))


Theoretical massNumber of molelcules
Total (without water)74,7002
Polymers74,7002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-90 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.127, 104.437, 111.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ketol-acid reductoisomerase (NADP(+)) / KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / ...KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / Ketol-acid reductoisomerase type 1 / Ketol-acid reductoisomerase type I


Mass: 37350.195 Da / Num. of mol.: 2 / Mutation: E195S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria)
Strain: D39 / NCTC 7466 / Gene: ilvC, SPD_0406 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q04M32, ketol-acid reductoisomerase (NADP+)
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.0, 0.1 M NaCl, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→43.43 Å / Num. obs: 53173 / % possible obs: 99.8 % / Redundancy: 13.6 % / Biso Wilson estimate: 27.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 68.9
Reflection shellResolution: 2.02→2.1 Å / Num. unique obs: 2617 / CC1/2: 0.974

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L2I

6l2i


Resolution: 2.02→43.42 Å / SU ML: 0.2321 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.4153
RfactorNum. reflection% reflection
Rfree0.2667 2695 5.08 %
Rwork0.2304 --
obs0.2322 53090 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.15 Å2
Refinement stepCycle: LAST / Resolution: 2.02→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4990 0 0 0 4990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745084
X-RAY DIFFRACTIONf_angle_d0.84566868
X-RAY DIFFRACTIONf_chiral_restr0.0533748
X-RAY DIFFRACTIONf_plane_restr0.0058908
X-RAY DIFFRACTIONf_dihedral_angle_d3.02733040
LS refinement shellResolution: 2.02→2.06 Å
RfactorNum. reflection% reflection
Rfree0.2986 134 -
Rwork0.2604 2500 -
obs--95.43 %

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