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- PDB-9l8r: Dihydroxyacid dehydratase (DHAD) -

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Basic information

Entry
Database: PDB / ID: 9l8r
TitleDihydroxyacid dehydratase (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 / pollen development / root 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 / pollen development / root 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 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: 2.19 Å
AuthorsZhou, J. / Liu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The mutant structure of DHAD
Authors: Zhou, J. / Liu, D.
History
DepositionDec 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 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)61,4024
Polymers60,9371
Non-polymers4653
Water4,035224
1
A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules

A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8048
Polymers121,8732
Non-polymers9316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area8340 Å2
ΔGint-76 kcal/mol
Surface area36200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.040, 136.040, 66.829
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-716-

HOH

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Components

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


Mass: 60936.539 Da / Num. of mol.: 1
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: Chemical ChemComp-A1L7A / (2~{R})-7-fluoranyl-2-oxidanyl-3-oxidanylidene-4-prop-2-ynyl-1,4-benzoxazine-2-carboxylic acid


Mass: 265.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8FNO5 / 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.: 224 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 5.0, 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97877 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
ReflectionResolution: 2.19→39.04 Å / Num. obs: 32804 / % possible obs: 99.93 % / Redundancy: 13.1 % / Biso Wilson estimate: 28.55 Å2 / CC1/2: 0.933 / Net I/σ(I): 2.2
Reflection shellResolution: 2.19→2.26 Å / Num. unique obs: 2782 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YM0

5ym0


Resolution: 2.19→39.04 Å / SU ML: 0.2436 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5296
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 1692 5.16 %
Rwork0.1841 31112 -
obs0.1865 32804 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.55 Å2
Refinement stepCycle: LAST / Resolution: 2.19→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 24 224 4479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844337
X-RAY DIFFRACTIONf_angle_d1.01235868
X-RAY DIFFRACTIONf_chiral_restr0.0507662
X-RAY DIFFRACTIONf_plane_restr0.0056766
X-RAY DIFFRACTIONf_dihedral_angle_d5.20423641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.30721320.23492538X-RAY DIFFRACTION100
2.25-2.330.27321340.22222559X-RAY DIFFRACTION100
2.33-2.410.2621280.20942554X-RAY DIFFRACTION99.7
2.41-2.510.27331520.1982531X-RAY DIFFRACTION100
2.51-2.620.27921430.1942574X-RAY DIFFRACTION100
2.62-2.760.25371310.19422568X-RAY DIFFRACTION100
2.76-2.930.24731350.18682571X-RAY DIFFRACTION100
2.93-3.160.25531350.18532599X-RAY DIFFRACTION100
3.16-3.480.22491460.18182582X-RAY DIFFRACTION99.93
3.48-3.980.19471550.16372610X-RAY DIFFRACTION100
3.98-5.010.20191710.15512619X-RAY DIFFRACTION99.96
5.01-39.040.2131300.19442807X-RAY DIFFRACTION99.56

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