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- PDB-7ysm: Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) co-crystal... -

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Basic information

Entry
Database: PDB / ID: 7ysm
TitleCrystal Structure of UDP-glucose 4-epimerase (Rv3634c) co-crystallized with UDP-N-acetylglucosamine from Mycobacterium tuberculosis
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / GalE1 / UDP-N-acetylgalactosamine / UDP-N-acetylglucosamine
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / plasma membrane
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Short-chain dehydrogenases/reductases family signature. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsYadav, S. / Bhatia, I. / Biswal, B.K.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchR.12014/03/2019-HR India
CitationJournal: To Be Published
Title: Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) co-crystallized with UDP-N-acetylglucosamine from Mycobacterium tuberculosis
Authors: Yadav, S. / Bhatia, I. / Biswal, B.K.
History
DepositionAug 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,5678
Polymers68,9072
Non-polymers2,6606
Water14,502805
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-51 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.114, 76.414, 79.949
Angle α, β, γ (deg.)90.000, 91.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34453.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: galE1, Rv3634c / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: P9WN67, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Tris pH 8.5 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 51063 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.058 / Rrim(I) all: 0.156 / Χ2: 1.065 / Net I/σ(I): 5.7 / Num. measured all: 371335
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.791 / Num. unique obs: 2548 / CC1/2: 0.733 / Rpim(I) all: 0.348 / Rrim(I) all: 0.867 / Χ2: 0.793 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YS8

7ys8


Resolution: 1.87→31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.1472 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 2677 5.2 %RANDOM
Rwork0.1617 ---
obs0.1635 48365 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.19 Å2 / Biso mean: 19.547 Å2 / Biso min: 9.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20.03 Å2
2--0.11 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 1.87→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4671 0 174 806 5651
Biso mean--16.67 31.4 -
Num. residues----622
Refine LS restraintsType: r_bond_refined_d / Dev ideal: 0.003 / Dev ideal target: 0.012 / Number: 5118
LS refinement shellResolution: 1.87→1.915 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.298 160 -
Rwork0.276 3507 -
obs--96.78 %

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