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- PDB-7ys8: Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) from Mycob... -

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Basic information

Entry
Database: PDB / ID: 7ys8
TitleCrystal Structure of UDP-glucose 4-epimerase (Rv3634c) 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 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) from Mycobacterium tuberculosis
Authors: Yadav, S. / Bhatia, I. / Biswal, B.K.
History
DepositionAug 11, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 16, 2023ID: 6LTT
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)70,3856
Polymers68,9072
Non-polymers1,4784
Water13,781765
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-39 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.866, 76.850, 80.124
Angle α, β, γ (deg.)90.000, 91.440, 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: AH37Rv / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
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: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 40386 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.07 / Rrim(I) all: 0.164 / Χ2: 1.413 / Net I/σ(I): 6.7 / Num. measured all: 215119
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Num. unique obs: 1843 / CC1/2: 0.735 / Rpim(I) all: 0.333 / Rrim(I) all: 0.699 / Χ2: 1.146 / % possible all: 92.1

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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: 4ZRM

4zrm


Resolution: 2.02→25.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.704 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 2114 5.2 %RANDOM
Rwork0.1563 ---
obs0.1588 38254 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.78 Å2 / Biso mean: 23.135 Å2 / Biso min: 12.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.2 Å2
2--0.09 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.02→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 98 765 5529
Biso mean--17.18 33.88 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124919
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.6386735
LS refinement shellResolution: 2.021→2.074 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 166 -
Rwork0.257 2697 -
all-2863 -
obs--97.48 %

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