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- PDB-9jsq: The mutant structure of Dihydroxyacid dehydratase (DHAD)-I177F -

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Basic information

Entry
Database: PDB / ID: 9jsq
TitleThe mutant structure of Dihydroxyacid dehydratase (DHAD)-I177F
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: 2.45 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
DepositionOct 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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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)61,8652
Polymers61,6891
Non-polymers1761
Water32418
1
A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules

A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7304
Polymers123,3792
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area7980 Å2
ΔGint-63 kcal/mol
Surface area36630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.490, 135.490, 66.860
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

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Components

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


Mass: 61689.371 Da / Num. of mol.: 1 / Mutation: I177F, 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-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
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: 0.97853 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.45→47.59 Å / Num. obs: 22544 / % possible obs: 96.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 46.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.071 / Net I/σ(I): 9.4
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 5 % / Rmerge(I) obs: 0.792 / Num. unique obs: 2562 / CC1/2: 0.593 / % possible all: 98.8

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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: 2.45→38.94 Å / SU ML: 0.2825 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2327 1125 5 %
Rwork0.1976 21366 -
obs0.1994 22491 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.66 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 4 18 4119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024215
X-RAY DIFFRACTIONf_angle_d0.53745696
X-RAY DIFFRACTIONf_chiral_restr0.0401647
X-RAY DIFFRACTIONf_plane_restr0.0042744
X-RAY DIFFRACTIONf_dihedral_angle_d4.347596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.560.34321390.27362695X-RAY DIFFRACTION98.4
2.56-2.70.29861340.25322668X-RAY DIFFRACTION97.56
2.7-2.870.29131360.23982650X-RAY DIFFRACTION97.17
2.87-3.090.27561410.22972706X-RAY DIFFRACTION97.8
3.09-3.40.22351270.20472677X-RAY DIFFRACTION96.82
3.4-3.890.20671380.18722622X-RAY DIFFRACTION94.04
3.89-4.90.19641430.1582664X-RAY DIFFRACTION94.77
4.9-38.940.22661670.19092684X-RAY DIFFRACTION91.2
Refinement TLS params.Method: refined / Origin x: 37.6050743837 Å / Origin y: -12.5213369073 Å / Origin z: -1.28985207752 Å
111213212223313233
T0.255623569766 Å2-0.0267786244396 Å20.00644748703751 Å2-0.259432995213 Å20.00575583574435 Å2--0.275971083777 Å2
L0.463966984589 °20.104210004418 °20.000220355400035 °2-0.67214497689 °2-0.193061162568 °2--0.574390892086 °2
S0.017486554736 Å °-0.0556593770355 Å °0.0474674984621 Å °0.0136781133623 Å °0.016041294819 Å °-0.125347827987 Å °-0.0615357081378 Å °0.0720842365308 Å °-7.69425632344E-6 Å °
Refinement TLS groupSelection details: all

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