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- PDB-8ej0: Crystal structure of Fe-S cluster-dependent dehydratase from Para... -

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Basic information

Entry
Database: PDB / ID: 8ej0
TitleCrystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg
ComponentsDihydroxyacid dehydratase
KeywordsLYASE / Fe-S dehydratase / sugar-acid dehydratase / ilvd/EDD family / DHAD
Function / homology
Function and homology information


hydro-lyase activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
: / : / 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
BICARBONATE ION / CARBON DIOXIDE / FE2/S2 (INORGANIC) CLUSTER / Dihydroxyacid dehydratase
Similarity search - Component
Biological speciesParalcaligenes ureilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBayaraa, T. / Lonhienne, T. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210101802 Australia
CitationJournal: Chemistry / Year: 2023
Title: Structural and Functional Insight into the Mechanism of the Fe-S Cluster-Dependent Dehydratase from Paralcaligenes ureilyticus.
Authors: Bayaraa, T. / Lonhienne, T. / Sutiono, S. / Melse, O. / Bruck, T.B. / Marcellin, E. / Bernhardt, P.V. / Boden, M. / Harmer, J.R. / Sieber, V. / Guddat, L.W. / Schenk, G.
History
DepositionSep 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Sep 11, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroxyacid dehydratase
C: Dihydroxyacid dehydratase
E: Dihydroxyacid dehydratase
G: Dihydroxyacid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,81819
Polymers250,6074
Non-polymers1,21115
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26480 Å2
ΔGint-190 kcal/mol
Surface area60110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.908, 178.071, 92.858
Angle α, β, γ (deg.)90.000, 101.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ACEG

#1: Protein
Dihydroxyacid dehydratase


Mass: 62651.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paralcaligenes ureilyticus (bacteria) / Gene: EDC26_11947 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4R3LQ44

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Non-polymers , 5 types, 146 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium/potassium phosphate, 0.1 M Bis-Tris-Propane (BTP) pH 8.5, 20% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.59→48.16 Å / Num. obs: 68328 / % possible obs: 99.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.041 / Net I/σ(I): 10.8
Reflection shellResolution: 2.59→2.65 Å / Rmerge(I) obs: 0.598 / Num. unique obs: 4514 / R split: 1.8 / Rpim(I) all: 0.282

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J84

5j84


Resolution: 2.59→44.05 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1998 2.93 %
Rwork0.1938 66262 -
obs0.1951 68260 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.17 Å2 / Biso mean: 51.8332 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.59→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17237 0 47 131 17415
Biso mean--54.17 43.84 -
Num. residues----2272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.59-2.660.3381390.2924633477298
2.66-2.730.33691440.275147404884100
2.73-2.810.31041430.258547654908100
2.81-2.90.31971440.255147614905100
2.9-30.33781420.251146974839100
3-3.120.27161410.24284717485899
3.12-3.270.28211440.23994726487099
3.27-3.440.29321420.22514724486699
3.44-3.650.26131410.19684681482298
3.65-3.940.24161430.178947384881100
3.94-4.330.19361440.157547774921100
4.33-4.960.16751440.145447724916100
4.96-6.240.18571440.172147664910100
6.24-44.050.20661430.15624765490899

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