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

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Basic information

Entry
Database: PDB / ID: 8epz
TitleCrystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mn
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: 2.6 Å
AuthorsBayaraa, T. / Lonhienne, T. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210101802 Australia
CitationJournal: To Be Published
Title: Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg
Authors: Bayaraa, T. / Lonhienne, T. / Guddat, L.W.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroxyacid dehydratase
B: Dihydroxyacid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,95810
Polymers125,3032
Non-polymers6558
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-85 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.639, 113.135, 182.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydroxyacid dehydratase


Mass: 62651.746 Da / Num. of mol.: 2
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, 78 molecules

#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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M succinic acid, 15% 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: 2.6→48.107 Å / Num. obs: 44640 / % possible obs: 98.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.987 Å / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3904 / Rpim(I) all: 0.316

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EJ0

8ej0


Resolution: 2.6→48.107 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1390 4.48 %
Rwork0.2102 29616 -
obs0.2121 31006 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.05 Å2 / Biso mean: 61.2977 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.6→48.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8605 0 23 70 8698
Biso mean--66.58 55.65 -
Num. residues----1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058806
X-RAY DIFFRACTIONf_angle_d0.72811924
X-RAY DIFFRACTIONf_chiral_restr0.0441316
X-RAY DIFFRACTIONf_plane_restr0.0041579
X-RAY DIFFRACTIONf_dihedral_angle_d22.6683255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.69290.40151350.3369292699
2.6929-2.80070.40011380.3061291099
2.8007-2.92820.35881370.2843292099
2.9282-3.08250.32891390.2697295299
3.0825-3.27560.31651380.2422935100
3.2756-3.52850.26521380.2249295399
3.5285-3.88340.23361380.1957293599
3.8834-4.4450.22921390.1755297199
4.445-5.59890.1961420.168299099
5.5989-48.1070.18261460.17453124100

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