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- PDB-6k0h: Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium... -

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Basic information

Entry
Database: PDB / ID: 6k0h
TitleCrystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / Rossmann fold / HYDROLASE
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 / DI(HYDROXYETHYL)ETHER / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)39,8737
Polymers38,3411
Non-polymers1,5326
Water3,801211
1
A: UDP-glucose 4-epimerase
hetero molecules

A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,74514
Polymers76,6822
Non-polymers3,06312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7500 Å2
ΔGint-49 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.450, 69.450, 321.986
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#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: galE, 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

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Non-polymers , 5 types, 217 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% (v/v) PEG400, 0.2 M MgCl, 0.1 M HEPES-NaOH (pH 7.5), and 10 mM UDP-GlcNAc

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2014
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→50 Å / Num. obs: 32699 / % possible obs: 100 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 28.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 17 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1585 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EK6

1ek6


Resolution: 2→34.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.138
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1649 5.1 %RANDOM
Rwork0.1812 ---
obs0.1832 30845 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.59 Å2 / Biso mean: 33.788 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 99 211 2898
Biso mean--34.53 43.48 -
Num. residues----335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0142750
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172476
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.7053753
X-RAY DIFFRACTIONr_angle_other_deg1.4921.6755791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64923.821123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61915428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.597159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023018
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02500
LS refinement shellResolution: 1.996→2.048 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 115 -
Rwork0.24 2212 -
all-2327 -
obs--98.64 %

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