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- PDB-6k0g: Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium... -

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Basic information

Entry
Database: PDB / ID: 6k0g
TitleCrystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / Rossmann fold
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNam, Y.-W. / Nishimoto, M. / Arakawa, T. / Kitaoka, M. / Fushinobu, S.
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum.
Authors: Nam, Y.W. / Nishimoto, M. / Arakawa, T. / Kitaoka, M. / Fushinobu, S.
History
DepositionMay 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,4334
Polymers38,3411
Non-polymers1,0923
Water6,756375
1
A: UDP-glucose 4-epimerase
hetero molecules

A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8668
Polymers76,6822
Non-polymers2,1846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6010 Å2
ΔGint-60 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.235, 70.235, 320.578
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein UDP-glucose 4-epimerase / UDP-galactose 4-epimerase


Mass: 38341.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b) (bacteria)
Strain: ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b
Gene: lnpD, BLLJ_1620 / Variant: JCM 1217 / Plasmid: pET-30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus (DE3)-RIL / References: UniProt: E8MF10, UDP-glucose 4-epimerase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% (v/v) PEG 400, 0.2 M MgCl, 0.1 M HEPES-NaOH (pH 7.5), 10 mM UDP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 5, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 44804 / % possible obs: 100 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 31.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 20.6 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 2104 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EK6

1ek6


Resolution: 1.8→40.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.697 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 2250 5 %RANDOM
Rwork0.1489 ---
obs0.1505 42417 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.58 Å2 / Biso mean: 21.326 Å2 / Biso min: 6.63 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 70 375 3033
Biso mean--16.98 33.03 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0142723
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172447
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.6943721
X-RAY DIFFRACTIONr_angle_other_deg1.0891.6595721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64623.821123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55815428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.965159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
LS refinement shellResolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 165 -
Rwork0.162 2994 -
all-3159 -
obs--97.92 %

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