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

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Basic information

Entry
Database: PDB / ID: 7ysa
TitleCrystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex with UDP-glucose in chain A and UDP-galactose in chain B from Mycobacterium tuberculosis
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / GalE1
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 / 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 / Resolution: 1.95 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 UDP-glucose in chainA and UDP-galactose in chain B 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

Downloads & links

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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)71,61210
Polymers68,9072
Non-polymers2,7058
Water14,088782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-47 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.222, 76.452, 79.961
Angle α, β, γ (deg.)90.000, 91.970, 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: H37Rv / Gene: galE1 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: P9WN67, UDP-glucose 4-epimerase

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Non-polymers , 6 types, 790 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 44546 / % possible obs: 98.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.052 / Rrim(I) all: 0.118 / Χ2: 1.168 / Net I/σ(I): 8.2 / Num. measured all: 224951
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.489 / Num. unique obs: 3852 / CC1/2: 0.79 / Rpim(I) all: 0.29 / Rrim(I) all: 0.573 / Χ2: 0.851 / % possible all: 85.8

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Processing

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

7ys8


Resolution: 1.95→28.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2086 / WRfactor Rwork: 0.1671 / FOM work R set: 0.8676 / SU R Cruickshank DPI: 0.179 / SU Rfree: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 2246 5 %RANDOM
Rwork0.1671 ---
obs0.1691 42422 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.94 Å2 / Biso mean: 21.271 Å2 / Biso min: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.48 Å2
2--0.51 Å20 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.95→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 176 782 5635
Biso mean--20.53 32.29 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125037
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.6456907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.07920.655275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68815707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5581547
X-RAY DIFFRACTIONr_chiral_restr0.0760.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023911
LS refinement shellResolution: 1.95→1.996 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.353 146 -
Rwork0.308 2623 -
obs--83.05 %

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