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- PDB-6c5n: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -

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Basic information

Entry
Database: PDB / ID: 6c5n
TitleCrystal structure of Staphylococcus aureus ketol-acid reductoisomerase with hydroxyoxamate inhibitor 1
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsOXIDOREDUCTASE / ketol-acid reductoisomerase / isomerase / inhibitor
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
ProC C-terminal domain-like fold / ProC C-terminal domain-like fold - #10 / 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. ...ProC C-terminal domain-like fold / ProC C-terminal domain-like fold - #10 / 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 / Helix non-globular / Special / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(cyclopentylamino)(oxo)acetic acid / [cyclopentyl(hydroxy)amino](oxo)acetic acid / IMIDAZOLE / Chem-NDP / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.673 Å
AuthorsKandale, A. / Patel, K.M. / Zheng, S. / You, L. / Guddat, L.W. / Schenk, G. / Schembri, M.A. / McGeary, R.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Design, synthesis, in vitro activity and crystallisation of novel N-isopropyl-N-hydroxyoxamate derivatives as ketol-acid reductosiomerase (KARI) inhibitor
Authors: Kandale, A. / Patel, K.M. / Zheng, S. / You, L. / Guddat, L.W. / Schenk, G. / Schembri, M.A. / McGeary, R.P.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,82913
Polymers75,5112
Non-polymers2,31811
Water15,061836
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15890 Å2
ΔGint-146 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.480, 80.394, 67.304
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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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: 37755.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: ilvC, SAB1941 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q2YUF3, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 6 types, 847 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EN4 / [cyclopentyl(hydroxy)amino](oxo)acetic acid


Mass: 173.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO4
#5: Chemical ChemComp-81B / (cyclopentylamino)(oxo)acetic acid


Mass: 157.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO3
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Imidazole pH8 17.5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.67→46.63 Å / Num. obs: 79180 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Net I/σ(I): 13.2
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3915 / Rpim(I) all: 0.322 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W3K

5w3k


Resolution: 1.673→46.613 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 17.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 2025 2.56 %
Rwork0.1546 --
obs0.1556 79149 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.673→46.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 151 836 6077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015491
X-RAY DIFFRACTIONf_angle_d1.1857456
X-RAY DIFFRACTIONf_dihedral_angle_d5.5064425
X-RAY DIFFRACTIONf_chiral_restr0.086795
X-RAY DIFFRACTIONf_plane_restr0.007995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6727-1.71460.23031550.20245373X-RAY DIFFRACTION98
1.7146-1.76090.25541520.19895504X-RAY DIFFRACTION100
1.7609-1.81270.231400.20035474X-RAY DIFFRACTION100
1.8127-1.87120.26121450.19115537X-RAY DIFFRACTION100
1.8712-1.93810.25521400.17745473X-RAY DIFFRACTION100
1.9381-2.01570.19671510.16295531X-RAY DIFFRACTION100
2.0157-2.10750.19351500.16135456X-RAY DIFFRACTION100
2.1075-2.21860.21611390.15565494X-RAY DIFFRACTION100
2.2186-2.35760.20691440.15665515X-RAY DIFFRACTION100
2.3576-2.53960.20351400.15835500X-RAY DIFFRACTION100
2.5396-2.79510.20451350.15625562X-RAY DIFFRACTION100
2.7951-3.19950.19411430.15025540X-RAY DIFFRACTION100
3.1995-4.03070.1611360.13335562X-RAY DIFFRACTION100
4.0307-46.63060.14381550.1345603X-RAY DIFFRACTION100

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