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- PDB-6l2i: IlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_WT -

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Basic information

Entry
Database: PDB / ID: 6l2i
TitleIlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_WT
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsISOMERASE / IlvC / Stereptococcus pneumoniae / BCAA pathway / ketol-acid reductoisomerase
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
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,27423
Polymers74,7842
Non-polymers2,48921
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16690 Å2
ΔGint-267 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.063, 104.349, 110.942
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

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Protein , 1 types, 2 molecules AB

#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: 37392.230 Da / Num. of mol.: 2
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 (E. coli)
References: UniProt: Q04M32, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 5 types, 689 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.1M NaCl 1.5 M Amminoum 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: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→41.63 Å / Num. obs: 88937 / % possible obs: 98.98 % / Redundancy: 14.4 % / Biso Wilson estimate: 23.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rrim(I) all: 0.071 / Net I/σ(I): 58.1
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 6.16 / Num. unique obs: 8757 / CC1/2: 0.98 / Rpim(I) all: 0.126 / Rrim(I) all: 0.486

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Coot1.16_3549model building
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NP3

1np3


Resolution: 1.69→41.63 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2086 2005 -
Rwork0.1942 --
obs-88863 98.9 %
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.69→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4989 0 148 668 5805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735295
X-RAY DIFFRACTIONf_angle_d1.08757173
X-RAY DIFFRACTIONf_chiral_restr0.0531769
X-RAY DIFFRACTIONf_plane_restr0.0048929
X-RAY DIFFRACTIONf_dihedral_angle_d13.84033167
LS refinement shellResolution: 1.693→1.753 Å
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.2365 8734 -
obs--98.81 %

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