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- PDB-9ix7: Crystal structure of homolog of dihydroxyacid dehydratase(AstD) f... -

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Basic information

Entry
Database: PDB / ID: 9ix7
TitleCrystal structure of homolog of dihydroxyacid dehydratase(AstD) from Aspergillus terreus
Componentsdihydroxy-acid dehydratase
KeywordsLYASE / dihydroxyacid dehydratase
Function / homology
Function and homology information


dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / L-valine biosynthetic process / isoleucine biosynthetic process / 2 iron, 2 sulfur cluster binding / mitochondrion / metal ion binding
Similarity search - Function
: / Dihydroxy-acid/6-phosphogluconate dehydratase C-terminal / 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
DI(HYDROXYETHYL)ETHER / dihydroxy-acid dehydratase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHuang, W.X. / Zhang, P.X. / Zhou, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071446 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
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dihydroxy-acid dehydratase
B: dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6846
Polymers120,3922
Non-polymers2924
Water6,251347
1
A: dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3643
Polymers60,1961
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3203
Polymers60,1961
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-16 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.614, 66.278, 268.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU(chain 'A' and (resid 69 through 79 or (resid 80...AA69 - 8231 - 44
12HISHISSERSER(chain 'A' and (resid 69 through 79 or (resid 80...AA91 - 11753 - 79
13LYSLYSILEILE(chain 'A' and (resid 69 through 79 or (resid 80...AA125 - 18587 - 147
14ALAALAARGARG(chain 'A' and (resid 69 through 79 or (resid 80...AA238 - 292200 - 254
15ALAALAILEILE(chain 'A' and (resid 69 through 79 or (resid 80...AA294 - 598256 - 560
16EDOEDOEDOEDO(chain 'A' and (resid 69 through 79 or (resid 80...AD602
27METMETGLUGLU(chain 'B' and (resid 69 through 160 or (resid 161...BB69 - 8231 - 44
28HISHISSERSER(chain 'B' and (resid 69 through 160 or (resid 161...BB91 - 11753 - 79
29LYSLYSILEILE(chain 'B' and (resid 69 through 160 or (resid 161...BB125 - 18587 - 147
210ALAALAARGARG(chain 'B' and (resid 69 through 160 or (resid 161...BB238 - 292200 - 254
211ALAALAILEILE(chain 'B' and (resid 69 through 160 or (resid 161...BB294 - 598256 - 560
212EDOEDOEDOEDO(chain 'B' and (resid 69 through 160 or (resid 161...BF602

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Components

#1: Protein dihydroxy-acid dehydratase


Mass: 60195.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: ATEIFO6365_0004000400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5M3YPM6, dihydroxy-acid dehydratase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: MMT pH4.0 ,17% PEG1500, 1mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→47.2 Å / Num. obs: 45340 / % possible obs: 96.97 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.81 Å2 / Rmerge(I) obs: 0.185 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.04 / Num. unique obs: 3599

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
PHASESphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YMO

5ymo
PDB Unreleased entry


Resolution: 2.29→47.2 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 2294 5.06 %
Rwork0.2008 43029 -
obs0.2023 45323 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.92 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6945 0 19 347 7311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247086
X-RAY DIFFRACTIONf_angle_d0.64179572
X-RAY DIFFRACTIONf_chiral_restr0.04571090
X-RAY DIFFRACTIONf_plane_restr0.0041247
X-RAY DIFFRACTIONf_dihedral_angle_d17.67024327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.340.31251060.2631960X-RAY DIFFRACTION72.47
2.34-2.390.26491420.25322389X-RAY DIFFRACTION89.03
2.39-2.450.28641200.25722639X-RAY DIFFRACTION95.34
2.45-2.520.29111580.24582658X-RAY DIFFRACTION98.26
2.52-2.590.24651440.24282730X-RAY DIFFRACTION99.48
2.59-2.680.28331290.24432750X-RAY DIFFRACTION99.79
2.68-2.770.26481470.24362729X-RAY DIFFRACTION99.86
2.77-2.880.29251410.2342768X-RAY DIFFRACTION99.86
2.88-3.020.2931600.22932732X-RAY DIFFRACTION99.93
3.02-3.170.23821480.2142748X-RAY DIFFRACTION99.93
3.17-3.370.20761560.20762758X-RAY DIFFRACTION99.9
3.37-3.630.22271430.19252780X-RAY DIFFRACTION99.86
3.63-40.22261550.17132779X-RAY DIFFRACTION99.86
4-4.580.20921450.16152803X-RAY DIFFRACTION99.59
4.58-5.770.18091460.16962846X-RAY DIFFRACTION99.37
5.77-47.20.19081540.17922960X-RAY DIFFRACTION98.48
Refinement TLS params.Method: refined / Origin x: 0.0595562265417 Å / Origin y: 6.54804493785 Å / Origin z: 31.1419449094 Å
111213212223313233
T0.222520945577 Å2-0.00256759500025 Å2-0.0172976587248 Å2-0.248502046999 Å2-0.0136053827726 Å2--0.228391428836 Å2
L0.367849604575 °2-0.0604462383379 °2-0.021940454197 °2-0.700424665132 °20.161548638389 °2--0.354390394662 °2
S-0.0204219121202 Å °-0.00539430134682 Å °-0.0520605925625 Å °0.071757091828 Å °0.0128060889427 Å °-0.0496334137097 Å °0.0404222911583 Å °-0.0470329445581 Å °0.00725955329206 Å °
Refinement TLS groupSelection details: all

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