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- PDB-8hs0: The mutant structure of DHAD V178W -

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Basic information

Entry
Database: PDB / ID: 8hs0
TitleThe mutant structure of DHAD V178W
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 / pollen development / branched-chain amino acid biosynthetic process / hydro-lyase activity / L-valine biosynthetic process / isoleucine biosynthetic process / plastid ...dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / embryo sac development / root development / pollen development / branched-chain amino acid biosynthetic process / hydro-lyase activity / L-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 / 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: 1.42 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
DepositionDec 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 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)61,5184
Polymers61,2261
Non-polymers2923
Water7,728429
1
A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules

A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0368
Polymers122,4522
Non-polymers5846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area8920 Å2
ΔGint-70 kcal/mol
Surface area36250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.920, 135.920, 66.350
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-1065-

HOH

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Components

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


Mass: 61225.891 Da / Num. of mol.: 1 / Mutation: V178W, K559A, K560A
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
#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-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion / 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: BL19U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.42→45.31 Å / Num. obs: 116848 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 21.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Net I/σ(I): 18
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 1.341 / Num. unique obs: 5736 / CC1/2: 0.651

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZE4

5ze4


Resolution: 1.42→42.98 Å / SU ML: 0.1667 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 5935 5.08 %
Rwork0.1811 110840 -
obs0.1819 116775 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.41 Å2
Refinement stepCycle: LAST / Resolution: 1.42→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 11 429 4682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694378
X-RAY DIFFRACTIONf_angle_d1.10115925
X-RAY DIFFRACTIONf_chiral_restr0.0831665
X-RAY DIFFRACTIONf_plane_restr0.0076774
X-RAY DIFFRACTIONf_dihedral_angle_d13.89321642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.3241970.32093654X-RAY DIFFRACTION99.95
1.44-1.450.33081870.29083654X-RAY DIFFRACTION99.97
1.45-1.470.25751900.26163648X-RAY DIFFRACTION99.97
1.47-1.490.25362160.24313641X-RAY DIFFRACTION99.92
1.49-1.510.25671940.23223658X-RAY DIFFRACTION100
1.51-1.530.24292320.22253619X-RAY DIFFRACTION100
1.53-1.550.23241980.19993638X-RAY DIFFRACTION100
1.55-1.570.21511860.19623674X-RAY DIFFRACTION100
1.57-1.60.23031900.20173668X-RAY DIFFRACTION99.97
1.6-1.630.21871680.20113692X-RAY DIFFRACTION99.97
1.63-1.650.23612260.20343640X-RAY DIFFRACTION99.97
1.65-1.680.21621880.20013652X-RAY DIFFRACTION100
1.68-1.720.21182200.19863637X-RAY DIFFRACTION100
1.72-1.750.18951720.20133699X-RAY DIFFRACTION100
1.75-1.790.23332070.20653669X-RAY DIFFRACTION100
1.79-1.830.2221930.19733676X-RAY DIFFRACTION100
1.83-1.880.23161780.19183678X-RAY DIFFRACTION100
1.88-1.930.2181970.19193673X-RAY DIFFRACTION99.95
1.93-1.980.19261810.18633723X-RAY DIFFRACTION100
1.98-2.050.20482190.18073662X-RAY DIFFRACTION100
2.05-2.120.19372060.18053688X-RAY DIFFRACTION100
2.12-2.210.1971880.17993722X-RAY DIFFRACTION100
2.21-2.310.20212150.18143681X-RAY DIFFRACTION100
2.31-2.430.21811930.1793722X-RAY DIFFRACTION100
2.43-2.580.1941920.17763717X-RAY DIFFRACTION100
2.58-2.780.17121850.17993768X-RAY DIFFRACTION100
2.78-3.060.21061910.17563752X-RAY DIFFRACTION100
3.06-3.50.16682080.17043786X-RAY DIFFRACTION100
3.5-4.410.15392040.14843819X-RAY DIFFRACTION99.93
4.41-42.980.20912140.18473930X-RAY DIFFRACTION98.32

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