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- PDB-8imu: Dihydroxyacid dehydratase (DHAD) mutant-V497F -

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Basic information

Entry
Database: PDB / ID: 8imu
TitleDihydroxyacid dehydratase (DHAD) mutant-V497F
ComponentsDihydroxy-acid dehydratase, chloroplastic
KeywordsLYASE / [2Fe-2S] cluster / aspterric acid / 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/6-phosphogluconate dehydratase C-terminal / 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
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / Dihydroxy-acid dehydratase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroxy-acid dehydratase, chloroplastic
B: Dihydroxy-acid dehydratase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0288
Polymers122,3742
Non-polymers6546
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-59 kcal/mol
Surface area33600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.120, 135.120, 136.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 46 or resid 48...
d_2ens_1(chain "B" and (resid 4 through 46 or resid 48...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERASPASPAA4 - 464 - 46
d_12ASPASPTHRTHRAA48 - 6548 - 65
d_13ASNASNLEULEUAA67 - 7367 - 73
d_14GLUGLUASNASNAA75 - 9275 - 92
d_15ILEILEILEILEAA94 - 10094 - 100
d_16METMETGLYGLYAA102 - 106102 - 106
d_17CYSCYSASPASPAA108 - 119108 - 119
d_18ILEILEPROPROAA121 - 137121 - 137
d_19PROPROASNASNAA144 - 552144 - 552
d_110GLYGLYGLUGLUAA554 - 574554 - 574
d_111FESFESFESFESAC601
d_112ACTACTACTACTAD602
d_113GOLGOLGOLGOLAE603
d_21SERSERASPASPBB4 - 464 - 46
d_22ASPASPTHRTHRBB48 - 6548 - 65
d_23ASNASNLEULEUBB67 - 7367 - 73
d_24GLUGLUASNASNBB75 - 9275 - 92
d_25ILEILEILEILEBB94 - 10094 - 100
d_26METMETGLYGLYBB102 - 106102 - 106
d_27CYSCYSASPASPBB108 - 119108 - 119
d_28ILEILEPROPROBB121 - 137121 - 137
d_29PROPROASNASNBB144 - 552144 - 552
d_210GLYGLYGLUGLUBB554 - 574554 - 574
d_211FESFESFESFESBF601
d_212ACTACTACTACTBG602
d_213GOLGOLGOLGOLBH603

NCS oper: (Code: givenMatrix: (-0.00054509852578, -0.999999804775, -0.000305479706559), (-0.99999924729, 0.000544762381128, 0.00109938792527), (-0.00109922129679, 0.000306078751358, -0.999999349014) ...NCS oper: (Code: given
Matrix: (-0.00054509852578, -0.999999804775, -0.000305479706559), (-0.99999924729, 0.000544762381128, 0.00109938792527), (-0.00109922129679, 0.000306078751358, -0.999999349014)
Vector: 0.00348071699508, -0.0132994044475, 0.946502765989)

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Components

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


Mass: 61186.852 Da / Num. of mol.: 2 / Mutation: K559A, K560A, V497F
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.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.65 %
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: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.93→48 Å / Num. obs: 95022 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.6
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.473 / Mean I/σ(I) obs: 2 / Num. unique obs: 4650 / CC1/2: 0.87 / % possible all: 99.9

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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: 1.93→48 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 4701 4.96 %
Rwork0.1816 89984 -
obs0.1829 94685 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.36 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7770 0 28 594 8392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00878132
X-RAY DIFFRACTIONf_angle_d1.038411006
X-RAY DIFFRACTIONf_chiral_restr0.05721246
X-RAY DIFFRACTIONf_plane_restr0.00851446
X-RAY DIFFRACTIONf_dihedral_angle_d6.07931164
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.256938704383 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.3371530.33542968X-RAY DIFFRACTION99.81
1.95-1.970.31861690.29792938X-RAY DIFFRACTION99.81
1.97-20.30771730.28052925X-RAY DIFFRACTION99.71
2-2.020.28541460.25772986X-RAY DIFFRACTION99.84
2.02-2.050.28791510.24682949X-RAY DIFFRACTION99.74
2.05-2.080.31921580.23212987X-RAY DIFFRACTION99.87
2.08-2.110.25561580.21362966X-RAY DIFFRACTION99.71
2.11-2.140.2521180.20243000X-RAY DIFFRACTION99.78
2.14-2.170.21551140.1953000X-RAY DIFFRACTION99.71
2.17-2.210.25991690.19552953X-RAY DIFFRACTION99.55
2.21-2.250.21741730.19262932X-RAY DIFFRACTION99.84
2.25-2.290.21911740.19272978X-RAY DIFFRACTION99.84
2.29-2.330.21431560.19112969X-RAY DIFFRACTION99.9
2.33-2.380.20931550.18472979X-RAY DIFFRACTION99.78
2.38-2.430.22391680.18742963X-RAY DIFFRACTION99.87
2.43-2.490.23691510.19142982X-RAY DIFFRACTION99.87
2.49-2.550.22741660.18752981X-RAY DIFFRACTION99.81
2.55-2.620.23811270.18573011X-RAY DIFFRACTION99.94
2.62-2.70.21021640.18333008X-RAY DIFFRACTION99.87
2.7-2.780.19951650.17662987X-RAY DIFFRACTION100
2.78-2.880.19381640.17692987X-RAY DIFFRACTION99.97
2.88-30.18771570.18043020X-RAY DIFFRACTION99.91
3-3.130.22941570.18253019X-RAY DIFFRACTION100
3.13-3.30.20851310.17843047X-RAY DIFFRACTION100
3.3-3.510.19121670.16553016X-RAY DIFFRACTION100
3.51-3.780.16431970.1593013X-RAY DIFFRACTION99.91
3.78-4.160.18751390.14593073X-RAY DIFFRACTION100
4.16-4.760.15341560.14083072X-RAY DIFFRACTION100
4.76-5.990.20451560.17883134X-RAY DIFFRACTION99.97
5.99-480.19871690.18923141X-RAY DIFFRACTION95.94
Refinement TLS params.Method: refined / Origin x: 24.7948686697 Å / Origin y: -24.9042737375 Å / Origin z: 0.532842918962 Å
111213212223313233
T0.193966339846 Å2-0.013873213689 Å20.00615529708653 Å2-0.191806112449 Å2-0.00828202556556 Å2--0.176757009122 Å2
L0.426245066541 °20.193551054089 °2-0.0631292124069 °2-0.491176870232 °2-0.0464980450977 °2--0.326976664908 °2
S-0.00267477822982 Å °0.0186171914785 Å °-0.0328960951317 Å °-0.0124645659248 Å °0.00194927697486 Å °-0.0247880058584 Å °-0.0230063665716 Å °-0.0344497939186 Å °-3.78039406246E-6 Å °
Refinement TLS groupSelection details: all

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