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- PDB-5ze4: The structure of holo- structure of DHAD complex with [2Fe-2S] cluster -

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Basic information

Entry
Database: PDB / ID: 5ze4
TitleThe structure of holo- structure of DHAD complex with [2Fe-2S] cluster
ComponentsDihydroxy-acid dehydratase, chloroplastic
KeywordsLYASE / [2Fe-2S] cluster / inhibit / BCAAbiosynthetic pathway
Function / homology
Function and homology information


dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / embryo sac development / pollen development / root development / branched-chain amino acid biosynthetic process / hydro-lyase activity / valine biosynthetic process / isoleucine biosynthetic process / plastid ...dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / embryo sac development / pollen development / root development / branched-chain amino acid biosynthetic process / hydro-lyase activity / valine biosynthetic process / isoleucine biosynthetic process / plastid / chloroplast stroma / response to salt stress / chloroplast / 2 iron, 2 sulfur cluster binding / copper ion binding
Similarity search - Function
Dihydroxy-acid dehydratase / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2. / Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dehydratase family
Similarity search - Domain/homology
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / Dihydroxy-acid dehydratase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsZhou, J. / Zang, X. / Tang, Y. / Yan, Y. / Gan, J. / Wu, L.
CitationJournal: Nature / Year: 2018
Title: Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action.
Authors: Yan, Y. / Liu, Q. / Zang, X. / Yuan, S. / Bat-Erdene, U. / Nguyen, C. / Gan, J. / Zhou, J. / Jacobsen, S.E. / Tang, Y.
History
DepositionFeb 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5557
Polymers61,0081
Non-polymers5476
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-58 kcal/mol
Surface area22140 Å2
Unit cell
Length a, b, c (Å)135.467, 135.467, 65.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydroxy-acid dehydratase, chloroplastic / / DAD


Mass: 61007.617 Da / Num. of mol.: 1 / Mutation: K559A, K600A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DHAD, ILVD, At3g23940, F14O13.13 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9LIR4, dihydroxy-acid dehydratase

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Non-polymers , 5 types, 123 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate pH 5.0, 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 36139 / % possible obs: 100 % / Redundancy: 25.1 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 2
Reflection shellResolution: 2.11→2.15 Å / Rmerge(I) obs: 1.24

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J83

5j83


Resolution: 2.11→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.783 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.21519 1709 4.9 %RANDOM
Rwork0.17272 ---
obs0.17479 33076 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.395 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.11→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 24 117 4359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194314
X-RAY DIFFRACTIONr_bond_other_d0.0020.024149
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9895834
X-RAY DIFFRACTIONr_angle_other_deg0.939612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63924.937158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81115749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2131520
X-RAY DIFFRACTIONr_chiral_restr0.0610.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02866
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2342.5582279
X-RAY DIFFRACTIONr_mcbond_other1.2312.5582277
X-RAY DIFFRACTIONr_mcangle_it1.6183.832845
X-RAY DIFFRACTIONr_mcangle_other1.6183.832846
X-RAY DIFFRACTIONr_scbond_it1.2212.7632035
X-RAY DIFFRACTIONr_scbond_other1.222.7642036
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5424.0692988
X-RAY DIFFRACTIONr_long_range_B_refined2.09820.084738
X-RAY DIFFRACTIONr_long_range_B_other2.01420.0544706
X-RAY DIFFRACTIONr_rigid_bond_restr1.02738459
X-RAY DIFFRACTIONr_sphericity_free28.22524
X-RAY DIFFRACTIONr_sphericity_bonded4.77658491
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 89 -
Rwork0.191 1964 -
obs--79.08 %
Refinement TLS params.Method: refined / Origin x: 38.147 Å / Origin y: -12.8445 Å / Origin z: -1.6749 Å
111213212223313233
T0.009 Å2-0.0109 Å20.0045 Å2-0.0221 Å2-0.0028 Å2--0.012 Å2
L0.1031 °20.1029 °2-0.0292 °2-0.3704 °2-0.1532 °2--0.2399 °2
S0.0151 Å °-0.0091 Å °0.0215 Å °0.0101 Å °-0.0026 Å °-0.0039 Å °-0.0246 Å °0.0489 Å °-0.0125 Å °

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