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- PDB-7yst: Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex... -

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Basic information

Entry
Database: PDB / ID: 7yst
TitleCrystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex with both UDP-glucose and UDP-galactose in chain B from Mycobacterium tuberculosis
ComponentsUDP-glucose 4-epimerase along with EC 5.1.3.2
KeywordsISOMERASE / GalE1
Function / homologydTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / GALACTOSE-URIDINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / NAD-dependent epimerase/dehydratase
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 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) in complex with both UDP-glucose and UDP-galactose in chain B from Mycobacterium tuberculosis
Authors: Yadav, S. / Bhatia, I. / Biswal, B.K.
History
DepositionAug 13, 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

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase along with EC 5.1.3.2
B: UDP-glucose 4-epimerase along with EC 5.1.3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,11910
Polymers68,9072
Non-polymers3,2128
Water16,520917
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-56 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.626, 81.385, 146.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-glucose 4-epimerase along with EC 5.1.3.2 / UDP-glucose 4-epimerase


Mass: 34453.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: galE1 / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: A0A045H759, dTDP-glucose 4,6-dehydratase

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Non-polymers , 5 types, 925 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 917 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.07 %
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 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 54985 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.043 / Rrim(I) all: 0.16 / Χ2: 1.139 / Net I/σ(I): 6.1 / Num. measured all: 765291
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.261 / Num. unique obs: 2713 / CC1/2: 0.762 / Rpim(I) all: 0.374 / Rrim(I) all: 1.317 / Χ2: 0.809 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7ys8


Resolution: 1.88→33.46 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2093 / WRfactor Rwork: 0.1654 / FOM work R set: 0.8677 / SU R Cruickshank DPI: 0.1461 / SU Rfree: 0.1358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 2687 4.9 %RANDOM
Rwork0.1654 ---
obs0.1675 52222 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 max: 60.89 Å2 / Biso mean: 24.573 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20 Å2
2--0.21 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.88→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 208 917 5821
Biso mean--23.4 35.95 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125250
X-RAY DIFFRACTIONr_angle_refined_deg0.921.6497234
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 199 -
Rwork0.289 3805 -
all-4004 -
obs--99.65 %

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