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- PDB-7ys9: Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex... -

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Basic information

Entry
Database: PDB / ID: 7ys9
TitleCrystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex with both UDP-Glucose and UDP-Galactose in chainA from Mycobacterium tuberculosis
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / GalE1 / UDP-glucose 4-epimerase / Rv3634c / UDP-Glucose / UDP-Galactose / Mycobacterium tuberculosis
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
GALACTOSE-URIDINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 chainA from Mycobacterium tuberculosis
Authors: Yadav, S. / Bhatia, I. / Biswal, B.K.
History
DepositionAug 11, 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)72,0579
Polymers68,9072
Non-polymers3,1507
Water16,195899
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-57 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.347, 76.851, 80.163
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: ATCC 25618 / H37Rv / Gene: galE1, Rv3634c / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: P9WN67, UDP-glucose 4-epimerase

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Non-polymers , 5 types, 906 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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
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 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→35 Å / Num. obs: 67055 / % possible obs: 89.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Χ2: 1.902 / Net I/σ(I): 24.4 / Num. measured all: 198448
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.156 / Num. unique obs: 6764 / CC1/2: 0.963 / Rpim(I) all: 0.106 / Rrim(I) all: 0.19 / Χ2: 1.162 / % possible all: 90.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7ys8


Resolution: 1.65→24.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 3406 5.1 %RANDOM
Rwork0.1861 ---
obs0.1875 63573 89.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.3 Å2 / Biso mean: 19.08 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å2-0 Å2-0.59 Å2
2--2.55 Å20 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.65→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 204 899 5784
Biso mean--15.14 29.53 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125125
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.6477049
LS refinement shellResolution: 1.65→1.692 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.308 239 -
Rwork0.259 4652 -
obs--89.25 %

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