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- PDB-5gy7: X-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from... -

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Basic information

Entry
Database: PDB / ID: 5gy7
TitleX-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from E.coli:evidence for existence of open and closed active site during catalysis.
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / Induced fit mechanism
Function / homology
Function and homology information


colanic acid biosynthetic process / racemase and epimerase activity, acting on carbohydrates and derivatives / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / galactose metabolic process / NAD+ binding / carbohydrate metabolic process / identical protein binding / cytoplasm / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NITRATE ION / URIDINE-5'-DIPHOSPHATE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsSingh, N. / Tiwari, P. / Phulera, S. / Dixit, A. / Choudhury, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyDBT- Builder BT/PR5006/INF/22/153/2012 India
CitationJournal: To Be Published
Title: X-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from E.coli:evidence for existence of open and closed active site during catalysis.
Authors: Singh, N. / Tiwari, P. / Phulera, S. / Dixit, A. / Choudhury, D.
History
DepositionSep 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)78,5138
Polymers76,2242
Non-polymers2,2896
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-41 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.110, 91.160, 80.260
Angle α, β, γ (deg.)90.00, 99.87, 90.00
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 / Galactowaldenase / UDP-galactose 4-epimerase


Mass: 38111.922 Da / Num. of mol.: 2 / Mutation: H243I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: galE, galD, b0759, JW0742 / Variant: W3110 / Plasmid: PET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P09147, UDP-glucose 4-epimerase

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Non-polymers , 5 types, 650 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Ammonium Nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→79.07 Å / Num. obs: 121857 / % possible obs: 98.7 % / Redundancy: 3.3 % / Net I/σ(I): 7.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XEL

1xel


Resolution: 1.43→79.07 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.729 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16014 6036 5 %RANDOM
Rwork0.13388 ---
obs0.13517 115821 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0.08 Å2
2---0.06 Å20 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.43→79.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 148 644 5934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0195426
X-RAY DIFFRACTIONr_bond_other_d0.0030.024947
X-RAY DIFFRACTIONr_angle_refined_deg2.4541.9797427
X-RAY DIFFRACTIONr_angle_other_deg1.157311349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03224.262237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92115786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9291529
X-RAY DIFFRACTIONr_chiral_restr0.1480.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216196
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021253
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2040.9012702
X-RAY DIFFRACTIONr_mcbond_other1.1810.92701
X-RAY DIFFRACTIONr_mcangle_it1.7581.3543374
X-RAY DIFFRACTIONr_mcangle_other1.7621.3553375
X-RAY DIFFRACTIONr_scbond_it2.0931.0552724
X-RAY DIFFRACTIONr_scbond_other2.0891.0542721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9321.5214051
X-RAY DIFFRACTIONr_long_range_B_refined4.27813.0696756
X-RAY DIFFRACTIONr_long_range_B_other4.03212.1026428
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.428→1.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 447 -
Rwork0.142 8417 -
obs--97.85 %

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