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- PDB-9evv: His579Leu variant of L-arabinonate dehydratase co-crystallized wi... -

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Basic information

Entry
Database: PDB / ID: 9evv
TitleHis579Leu variant of L-arabinonate dehydratase co-crystallized with 2-oxobutyrate
ComponentsL-arabinonate dehydratase
KeywordsLYASE / arabinonate dehydratase / IlvD/EDD superfamily / dihydroxy acid dehydratase / Weimberg/Dahms pathway / [2Fe-2S] cluster
Function / homology
Function and homology information


L-arabinonate dehydratase / D-fuconate dehydratase / D-fuconate dehydratase activity / L-arabinonate dehydratase activity / galactonate dehydratase / galactonate dehydratase activity / arabinose catabolic process / 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
2-KETOBUTYRIC ACID / FE2/S2 (INORGANIC) CLUSTER / L-arabinonate dehydratase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsRen, Y. / Rouvinen, J. / Hakulinen, N.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland322610 Finland
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: Unveiling the importance of the C-terminus in the sugar acid dehydratase of the IlvD/EDD superfamily.
Authors: Ren, Y. / Vettenranta, E. / Penttinen, L. / Blomster Andberg, M. / Koivula, A. / Rouvinen, J. / Hakulinen, N.
History
DepositionApr 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-arabinonate dehydratase
B: L-arabinonate dehydratase
C: L-arabinonate dehydratase
D: L-arabinonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,23813
Polymers255,3364
Non-polymers9039
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23570 Å2
ΔGint-200 kcal/mol
Surface area64540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.947, 148.211, 165.025
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

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Components

#1: Protein
L-arabinonate dehydratase / ArDHT / D-fuconate dehydratase / Galactonate dehydratase / L-arabonate dehydratase


Mass: 63833.945 Da / Num. of mol.: 4 / Mutation: H579L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: araD, Rleg2_2909 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B5ZZ34, L-arabinonate dehydratase, D-fuconate dehydratase, galactonate dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-2KT / 2-KETOBUTYRIC ACID / 2-OXOBUTANOIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM DTT (Dithiothreitol), 14 % (w/v) PEG 10000, 200 mM Ammonium acetate, 100 mM Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.44→48.48 Å / Num. obs: 98251 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.73 Å2 / CC1/2: 0.986 / Net I/σ(I): 5.66
Reflection shellResolution: 2.44→2.53 Å / Num. unique obs: 9397 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→48.48 Å / SU ML: 0.3338 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1999 2.04 %
Rwork0.1851 96219 -
obs0.186 98218 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.54 Å2
Refinement stepCycle: LAST / Resolution: 2.44→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17388 0 27 431 17846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007917766
X-RAY DIFFRACTIONf_angle_d0.991124063
X-RAY DIFFRACTIONf_chiral_restr0.05172678
X-RAY DIFFRACTIONf_plane_restr0.0083154
X-RAY DIFFRACTIONf_dihedral_angle_d7.71492507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.50.32891340.28986462X-RAY DIFFRACTION95.57
2.5-2.570.33321420.26676847X-RAY DIFFRACTION99.97
2.57-2.650.3271430.26136813X-RAY DIFFRACTION99.96
2.65-2.730.31511410.25866819X-RAY DIFFRACTION99.99
2.73-2.830.29441410.23736846X-RAY DIFFRACTION99.94
2.83-2.940.30251430.23636848X-RAY DIFFRACTION99.94
2.94-3.080.29341420.22846845X-RAY DIFFRACTION99.94
3.08-3.240.2571420.21166863X-RAY DIFFRACTION99.97
3.24-3.440.24591430.19026882X-RAY DIFFRACTION99.99
3.44-3.710.25221440.17016888X-RAY DIFFRACTION99.96
3.71-4.080.20611430.14816907X-RAY DIFFRACTION100
4.08-4.670.16811440.13116954X-RAY DIFFRACTION99.96
4.67-5.880.20411460.15436993X-RAY DIFFRACTION99.94

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