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- PDB-9jpi: The complex structure of DHAD with aspterric acid (AA). -

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Basic information

Entry
Database: PDB / ID: 9jpi
TitleThe complex structure of DHAD with aspterric acid (AA).
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: 2 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
DepositionSep 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: 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)62,4846
Polymers61,6551
Non-polymers8295
Water4,792266
1
A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules

A: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,96812
Polymers123,3112
Non-polymers1,65810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area9090 Å2
ΔGint-101 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.890, 135.890, 66.640
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-735-

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: 61655.355 Da / Num. of mol.: 1 / Mutation: 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

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Non-polymers , 5 types, 271 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K0O / Aspterric Acid / (1~{S},5~{S},8~{R},9~{R})-8-oxidanyl-4-propan-2-ylidene-10-oxatricyclo[7.2.1.0^{1,5}]dodecane-8-carboxylic acid


Mass: 266.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
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: 0.97852 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→47.58 Å / Num. obs: 42678 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.15 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.145 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.007 / Num. unique obs: 3089 / CC1/2: 0.725

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Processing

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

5ze4


Resolution: 2→47.58 Å / SU ML: 0.1968 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 2101 4.93 %
Rwork0.1817 40526 -
obs0.1833 42627 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.48 Å2
Refinement stepCycle: LAST / Resolution: 2→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 48 266 4541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844375
X-RAY DIFFRACTIONf_angle_d0.94785934
X-RAY DIFFRACTIONf_chiral_restr0.0511674
X-RAY DIFFRACTIONf_plane_restr0.0065768
X-RAY DIFFRACTIONf_dihedral_angle_d14.4451638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.29151270.24852646X-RAY DIFFRACTION99.93
2.05-2.10.27761380.23192658X-RAY DIFFRACTION100
2.1-2.150.2261100.21532693X-RAY DIFFRACTION99.96
2.15-2.220.24411370.21992664X-RAY DIFFRACTION100
2.22-2.290.26531260.21772687X-RAY DIFFRACTION99.93
2.29-2.370.25921410.21032662X-RAY DIFFRACTION100
2.37-2.470.24611760.19752644X-RAY DIFFRACTION100
2.47-2.580.22631480.18662661X-RAY DIFFRACTION100
2.58-2.710.21611380.18942692X-RAY DIFFRACTION100
2.71-2.880.22011350.18592708X-RAY DIFFRACTION99.89
2.88-3.110.24091330.1822691X-RAY DIFFRACTION99.96
3.11-3.420.21741530.17452709X-RAY DIFFRACTION100
3.42-3.910.18791560.15942728X-RAY DIFFRACTION99.93
3.91-4.930.15641460.1452757X-RAY DIFFRACTION99.69
4.93-47.580.21411370.18432926X-RAY DIFFRACTION99.55

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