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- PDB-6vo2: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -

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Basic information

Entry
Database: PDB / ID: 6vo2
TitleCrystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg, NADPH and inhibitor.
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsMETAL BINDING PROTEIN / reductoisomerase / inhibitor / complex
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / 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
Chem-NDP / 3-(methylsulfonyl)-2-oxopropanoic acid / Ketol-acid reductoisomerase (NADP(+)) / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBayaraa, T. / Patel, K.M. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)114729 Australia
CitationJournal: Chemistry / Year: 2020
Title: Discovery, Synthesis and Evaluation of a Ketol-Acid Reductoisomerase Inhibitor.
Authors: Bayaraa, T. / Kurz, J.L. / Patel, K.M. / Hussein, W.M. / Bilyj, J.K. / West, N.P. / Schenk, G. / McGeary, R.P. / Guddat, L.W.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 5, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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
Revision 1.3Oct 11, 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

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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)76,03610
Polymers74,1162
Non-polymers1,9208
Water12,845713
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint-143 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.039, 80.825, 66.803
Angle α, β, γ (deg.)90.000, 92.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37057.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ilvC, DB727_12700, E4U00_11130, ERS072840_02559, NCTC6133_02793, NCTC7878_02786, NCTC7988_02129
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A145BYP4, UniProt: Q2FWK4*PLUS, ketol-acid reductoisomerase (NADP+)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-R67 / 3-(methylsulfonyl)-2-oxopropanoic acid


Mass: 166.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 0.2M Sodium acetate pH 8.1 22.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 6, 2018 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.59→47.27 Å / Num. obs: 73135 / % possible obs: 80 % / Redundancy: 7.4 % / Biso Wilson estimate: 18.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Rrim(I) all: 0.077 / Net I/σ(I): 15.1 / Num. measured all: 538308
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allNet I/σ(I) obs% possible allCC1/2
1.59-1.621.20.41720170.4170.590.80.4
8.71-47.276.90.02240845910.0090.02451.999.10.999

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W3K

5w3k


Resolution: 1.59→45.164 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.4
RfactorNum. reflection% reflection
Rfree0.1999 1983 2.71 %
Rwork0.1631 --
obs0.1641 73102 80.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.98 Å2 / Biso mean: 23.0532 Å2 / Biso min: 9.5 Å2
Refinement stepCycle: final / Resolution: 1.59→45.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 120 713 5923
Biso mean--17.84 32.24 -
Num. residues----652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5903-1.63010.234321
1.6301-1.67410.228824
1.6741-1.72340.2634310.2404124320
1.7234-1.7790.25781770.22886331100
1.779-1.84260.24591710.21816329100
1.8426-1.91640.23851710.21346312100
1.9164-2.00360.21731650.19796334100
2.0036-2.10930.23141930.19196330100
2.1093-2.24140.22421790.17296310100
2.2414-2.41450.21421750.16626319100
2.4145-2.65740.20381830.16966364100
2.6574-3.04190.20471790.16386377100
3.0419-3.83210.18241750.14076353100
3.8321-45.1640.15641840.12776472100

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