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- PDB-5w3k: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -

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Basic information

Entry
Database: PDB / ID: 5w3k
TitleCrystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex NADPH, Mg2+ and CPD
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsISOMERASE / Ketol-acid reductisomerase
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-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
cyclopropane-1,1-dicarboxylic acid / Chem-NDP / Ketol-acid reductoisomerase (NADP(+)) / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å
AuthorsPatel, K.M. / Teran, D. / Zheng, S. / Kandale, A. / Schembri, M. / McGeary, R.P. / Schenk, G. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150104358 and FT120100694 Australia
CitationJournal: Chemistry / Year: 2017
Title: Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity.
Authors: Patel, K.M. / Teran, D. / Zheng, S. / Kandale, A. / Garcia, M. / Lv, Y. / Schembri, M.A. / McGeary, R.P. / Schenk, G. / Guddat, L.W.
History
DepositionJun 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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_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_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

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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)77,67012
Polymers75,7732
Non-polymers1,89710
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15980 Å2
ΔGint-163 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.941, 80.773, 66.748
Angle α, β, γ (deg.)90.00, 92.49, 90.00
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: 37886.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ilvC, BMF23_13825, BO217_1422, ERS072840_02559 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A0A145BYP4, UniProt: Q2FWK4*PLUS, ketol-acid reductoisomerase (NADP+)
#2: Chemical ChemComp-9TY / cyclopropane-1,1-dicarboxylic acid


Mass: 130.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M Sodium acetate pH8 22.5 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.0064
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 1.589→34.545 Å / Num. obs: 90047 / % possible obs: 98.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.025 / Net I/σ(I): 15.2
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4239 / Rpim(I) all: 0.285 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDZ

4xdz


Resolution: 1.589→34.545 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 18.46
RfactorNum. reflection% reflection
Rfree0.1866 1987 2.21 %
Rwork0.16 --
obs0.1606 90015 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.589→34.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 120 671 5881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095532
X-RAY DIFFRACTIONf_angle_d1.0577538
X-RAY DIFFRACTIONf_dihedral_angle_d5.9094441
X-RAY DIFFRACTIONf_chiral_restr0.06808
X-RAY DIFFRACTIONf_plane_restr0.007996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5888-1.62850.24531400.22656019X-RAY DIFFRACTION95
1.6285-1.67260.22691390.19656178X-RAY DIFFRACTION98
1.6726-1.72180.22811320.19666255X-RAY DIFFRACTION98
1.7218-1.77740.2271450.19286265X-RAY DIFFRACTION98
1.7774-1.84090.21951400.18846243X-RAY DIFFRACTION98
1.8409-1.91460.2241440.18386225X-RAY DIFFRACTION98
1.9146-2.00170.19341410.17046280X-RAY DIFFRACTION99
2.0017-2.10720.18851330.16526320X-RAY DIFFRACTION99
2.1072-2.23920.17731470.15716297X-RAY DIFFRACTION99
2.2392-2.41210.19191550.15416290X-RAY DIFFRACTION99
2.4121-2.65470.17571410.16056371X-RAY DIFFRACTION100
2.6547-3.03870.1881430.16256397X-RAY DIFFRACTION100
3.0387-3.82760.17241360.14546386X-RAY DIFFRACTION100
3.8276-34.55320.16121510.13786502X-RAY DIFFRACTION100

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