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- PDB-6l2s: IlvC, a ketol-acid reductoisomerase, from Streptococcus pneumonia... -

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Basic information

Entry
Database: PDB / ID: 6l2s
TitleIlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_D83G
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsISOMERASE / IlvC / Stereptococcus pneumoniae / BCAA pathway / ketol-acid reductoisomerase / D83G
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid 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 / Acetohydroxy acid isomeroreductase, catalytic 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: 2.29 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,6682
Polymers74,6682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-90 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.896, 68.516, 81.164
Angle α, β, γ (deg.)90.000, 94.584, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 37334.195 Da / Num. of mol.: 2 / Mutation: D83G
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+)

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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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.1 M NaCl, 1.8 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: 2.29→30.3 Å / Num. obs: 35335 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.997 / Net I/σ(I): 50
Reflection shellResolution: 2.29→2.37 Å / Num. unique obs: 1753 / CC1/2: 0.972

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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: 2.29→30.3 Å / SU ML: 0.2605 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1942
RfactorNum. reflection% reflection
Rfree0.2465 1769 5.01 %
Rwork0.209 --
obs0.2109 35316 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.3 Å2
Refinement stepCycle: LAST / Resolution: 2.29→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 0 0 4988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835082
X-RAY DIFFRACTIONf_angle_d0.94056864
X-RAY DIFFRACTIONf_chiral_restr0.0512746
X-RAY DIFFRACTIONf_plane_restr0.0059908
X-RAY DIFFRACTIONf_dihedral_angle_d3.15273036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.27871370.23182495X-RAY DIFFRACTION96.16
2.35-2.420.28051430.2332541X-RAY DIFFRACTION100
2.42-2.50.28581240.22392596X-RAY DIFFRACTION99.96
2.5-2.590.29141400.21232573X-RAY DIFFRACTION100
2.59-2.70.27721110.22872606X-RAY DIFFRACTION99.96
2.7-2.820.2721470.22942569X-RAY DIFFRACTION100
2.82-2.970.26761470.23742573X-RAY DIFFRACTION100
2.97-3.150.26691430.24192573X-RAY DIFFRACTION100
3.15-3.40.28771310.23232593X-RAY DIFFRACTION99.96
3.4-3.740.26461360.2062579X-RAY DIFFRACTION99.93
3.74-4.280.21271270.19252626X-RAY DIFFRACTION99.89
4.28-5.380.2171320.17362616X-RAY DIFFRACTION99.89
5.38-30.30.18511510.18382607X-RAY DIFFRACTION97.91

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