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- PDB-8ikz: The mutant structure of DHAD -

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Basic information

Entry
Database: PDB / ID: 8ikz
TitleThe mutant structure of DHAD
ComponentsDihydroxy-acid dehydratase, chloroplastic
KeywordsLYASE / [2Fe-2S] cluster / mutant / BCAA biosynthetic pathway
Function / homology
Function and homology information


dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / embryo sac development / root development / branched-chain amino acid biosynthetic process / pollen development / hydro-lyase activity / L-valine biosynthetic process / isoleucine biosynthetic process / chloroplast stroma ...dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / embryo sac development / root development / branched-chain amino acid biosynthetic process / pollen development / hydro-lyase activity / L-valine biosynthetic process / isoleucine biosynthetic process / chloroplast stroma / plastid / 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 C-terminal / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dihydroxy-acid/6-phosphogluconate dehydratase N-terminal
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Dihydroxy-acid dehydratase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZhou, J. / Zang, X. / Tang, Y. / Yan, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biodes Res / Year: 2024
Title: Structural Bases of Dihydroxy Acid Dehydratase Inhibition and Biodesign for Self-Resistance.
Authors: Zang, X. / Bat-Erdene, U. / Huang, W. / Wu, Z. / Jacobsen, S.E. / Tang, Y. / Zhou, J.
History
DepositionMar 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification

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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)61,7305
Polymers61,3421
Non-polymers3884
Water6,972387
1
A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules

A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,46110
Polymers122,6842
Non-polymers7778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area9560 Å2
ΔGint-126 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.580, 135.580, 66.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-1034-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 61342.094 Da / Num. of mol.: 1 / Mutation: V496W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DHAD, At3g23940, F14O13.13 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9LIR4, dihydroxy-acid dehydratase

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Non-polymers , 5 types, 391 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.75 %
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
PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→47.53 Å / Num. obs: 62203 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.788 / Num. unique obs: 3414 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZE4

5ze4


Resolution: 1.75→37.6 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 3004 4.83 %
Rwork0.1786 59155 -
obs0.1802 62159 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.5 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4229 0 16 387 4632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774364
X-RAY DIFFRACTIONf_angle_d1.0095908
X-RAY DIFFRACTIONf_chiral_restr0.0579666
X-RAY DIFFRACTIONf_plane_restr0.007772
X-RAY DIFFRACTIONf_dihedral_angle_d6.5053620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.31761410.2962815X-RAY DIFFRACTION99.66
1.78-1.810.31321490.27122793X-RAY DIFFRACTION99.46
1.81-1.840.30221380.24572795X-RAY DIFFRACTION99.63
1.84-1.880.26821270.22332794X-RAY DIFFRACTION98.95
1.88-1.920.2611360.22192800X-RAY DIFFRACTION98.96
1.92-1.960.27381320.21632817X-RAY DIFFRACTION99.83
1.96-20.23751520.2062792X-RAY DIFFRACTION99.7
2-2.050.2221440.21382817X-RAY DIFFRACTION99.46
2.05-2.110.22271440.19732803X-RAY DIFFRACTION99.46
2.11-2.170.24081330.1842812X-RAY DIFFRACTION99.46
2.17-2.240.21661280.17752816X-RAY DIFFRACTION98.69
2.24-2.320.21121570.18552800X-RAY DIFFRACTION99.23
2.32-2.410.18841470.1762821X-RAY DIFFRACTION99.2
2.41-2.520.20621640.17412799X-RAY DIFFRACTION99.2
2.52-2.660.23311410.18122835X-RAY DIFFRACTION98.61
2.66-2.820.22261260.18012829X-RAY DIFFRACTION98.6
2.82-3.040.24331510.17842790X-RAY DIFFRACTION97.19
3.04-3.350.2111430.17392816X-RAY DIFFRACTION97.98
3.35-3.830.19191460.16042851X-RAY DIFFRACTION97.94
3.83-4.820.14551600.13572799X-RAY DIFFRACTION95.82
4.83-37.60.21351450.17552961X-RAY DIFFRACTION95.33

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