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- PDB-6l2z: IlvC, a ketol-acid reductoisomerase, from Streptococcus pnuemonia... -

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Basic information

Entry
Database: PDB / ID: 6l2z
TitleIlvC, a ketol-acid reductoisomerase, from Streptococcus pnuemoniae_D191G
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsISOMERASE / IlvC / Stereptococcus pneumoniae / BCAA pathway / ketol-acid reductoisomerase / D191G
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / AMMONIUM ION / 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 7, 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 1.2Oct 23, 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)76,5509
Polymers74,6682
Non-polymers1,8817
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-128 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.880, 104.511, 112.478
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: 37334.195 Da / Num. of mol.: 2 / Mutation: D191G
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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Non-polymers , 5 types, 559 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 0.1 M NaCl, 1.5 M ammonium sulfate, 15% glycerol

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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 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→23.87 Å / Num. obs: 52903 / % possible obs: 98.1 % / Redundancy: 13.2 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.996 / Net I/σ(I): 54.6
Reflection shellResolution: 2.02→2.09 Å / Num. unique obs: 2650 / CC1/2: 0.993

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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→23.87 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7558
RfactorNum. reflection% reflection
Rfree0.2439 2682 5.09 %
Rwork0.2036 --
obs0.2057 52640 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.85 Å2
Refinement stepCycle: LAST / Resolution: 2.02→23.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 116 552 5656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745236
X-RAY DIFFRACTIONf_angle_d0.87817098
X-RAY DIFFRACTIONf_chiral_restr0.0539767
X-RAY DIFFRACTIONf_plane_restr0.0057924
X-RAY DIFFRACTIONf_dihedral_angle_d4.78284270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.060.30341460.232604X-RAY DIFFRACTION98.78
2.06-2.10.24891380.2192652X-RAY DIFFRACTION99.57
2.1-2.140.26861610.21932611X-RAY DIFFRACTION99.75
2.14-2.190.26991460.21332628X-RAY DIFFRACTION99.61
2.19-2.240.26931390.21272673X-RAY DIFFRACTION99.29
2.24-2.290.2611240.20762651X-RAY DIFFRACTION99.14
2.29-2.350.23321460.212623X-RAY DIFFRACTION99.11
2.35-2.420.26121420.20782642X-RAY DIFFRACTION99.36
2.42-2.50.24941710.20932659X-RAY DIFFRACTION99.65
2.5-2.590.24871310.19672661X-RAY DIFFRACTION99.57
2.59-2.70.22371470.20752661X-RAY DIFFRACTION99.72
2.7-2.820.24041300.2062676X-RAY DIFFRACTION99.61
2.82-2.970.27821500.2142676X-RAY DIFFRACTION99.37
2.97-3.150.2711440.22372678X-RAY DIFFRACTION99.54
3.15-3.390.26081410.20272688X-RAY DIFFRACTION99.05
3.39-3.730.1961380.18362629X-RAY DIFFRACTION96.92
3.73-4.270.1941270.17562553X-RAY DIFFRACTION93.38
4.27-5.370.22721260.1872536X-RAY DIFFRACTION91.13
5.37-23.870.27871350.23682457X-RAY DIFFRACTION85.49

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