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- PDB-8wop: Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase... -

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Basic information

Entry
Database: PDB / ID: 8wop
TitleCrystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase 2 (AtUGE2) complexed with UDP, wild-type
ComponentsUDP-glucose 4-epimerase 2
KeywordsISOMERASE
Function / homology
Function and homology information


salicylic acid binding / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / cell wall biogenesis / galactose metabolic process / cell wall organization / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / UDP-glucose 4-epimerase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMatsumoto, M. / Umezawa, A. / Kotake, T. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05495 Japan
Japan Society for the Promotion of Science (JSPS)23H02134 Japan
Japan Society for the Promotion of Science (JSPS)23H04302 Japan
Citation
Journal: Plant J. / Year: 2024
Title: Cytosolic UDP-L-arabinose synthesis by bifunctional UDP-glucose 4-epimerases in Arabidopsis.
Authors: Umezawa, A. / Matsumoto, M. / Handa, H. / Nakazawa, K. / Miyagawa, M. / Seifert, G.J. / Takahashi, D. / Fushinobu, S. / Kotake, T.
#1: Journal: Biochem J / Year: 2009
Title: Bifunctional cytosolic UDP-glucose 4-epimerases catalyse the interconversion between UDP-D-xylose and UDP-L-arabinose in plants.
Authors: Kotake, T. / Takata, R. / Verma, R. / Takaba, M. / Yamaguchi, D. / Orita, T. / Kaneko, S. / Matsuoka, K. / Koyama, T. / Reiter, W.D. / Tsumuraya, Y.
History
DepositionOct 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase 2
B: UDP-glucose 4-epimerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3336
Polymers81,1972
Non-polymers2,1354
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-43 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.309, 110.847, 65.552
Angle α, β, γ (deg.)90.00, 106.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-339-

TYR

21A-339-

TYR

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Components

#1: Protein UDP-glucose 4-epimerase 2


Mass: 40598.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UGE2,At4g23920 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q9T0A7
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20-22% (w/v) PEG3350 and 0.16-0.18 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2022
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→48.23 Å / Num. obs: 28665 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.062 / Net I/σ(I): 9.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2785 / CC1/2: 0.728 / Rpim(I) all: 0.374 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
MOLREP11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EK6

1ek6


Resolution: 2.35→48.23 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.3 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23591 1435 5 %RANDOM
Rwork0.17751 ---
obs0.18041 27229 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.142 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å21.65 Å2
2---2.76 Å20 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 2.35→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 138 43 5407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165083
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.6517487
X-RAY DIFFRACTIONr_angle_other_deg0.4761.57111714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2445672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.28534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45110881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021245
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3433.8822694
X-RAY DIFFRACTIONr_mcbond_other3.3423.8822694
X-RAY DIFFRACTIONr_mcangle_it4.866.9613361
X-RAY DIFFRACTIONr_mcangle_other4.8596.9613362
X-RAY DIFFRACTIONr_scbond_it3.9124.1832805
X-RAY DIFFRACTIONr_scbond_other3.9114.1822806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8317.5174126
X-RAY DIFFRACTIONr_long_range_B_refined7.24437.566128
X-RAY DIFFRACTIONr_long_range_B_other7.24537.576125
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 102 -
Rwork0.259 1998 -
obs--99.86 %

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