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- PDB-1gy8: Trypanosoma brucei UDP-galactose 4' epimerase -

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Basic information

Entry
Database: PDB / ID: 1gy8
TitleTrypanosoma brucei UDP-galactose 4' epimerase
ComponentsUDP-GALACTOSE 4-EPIMERASE
KeywordsOXIDOREDUCTASE / EPIMERASE / GALACTOSE / TRYPANOSOMA BRUCEI
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / glycosome / nucleotide binding / 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 / URIDINE-5'-DIPHOSPHATE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShaw, M.P. / Bond, C.S. / Hunter, W.N.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2003
Title: High-Resolution Crystal Structure of Trypanosoma Brucei Udp-Galactose 4'-Epimerase: A Potential Target for Structure-Based Development of Novel Trypanocides
Authors: Shaw, M.P. / Bond, C.S. / Roper, J.R. / Gourley, D.G. / Ferguson, M.A.J. / Hunter, W.N.
History
DepositionApr 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-GALACTOSE 4-EPIMERASE
B: UDP-GALACTOSE 4-EPIMERASE
C: UDP-GALACTOSE 4-EPIMERASE
D: UDP-GALACTOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,49712
Polymers175,2264
Non-polymers4,2708
Water23,1491285
1
A: UDP-GALACTOSE 4-EPIMERASE
B: UDP-GALACTOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7486
Polymers87,6132
Non-polymers2,1354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: UDP-GALACTOSE 4-EPIMERASE
D: UDP-GALACTOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7486
Polymers87,6132
Non-polymers2,1354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.185, 112.533, 160.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.30257, 0.792, 0.53027), (0.81494, -0.07355, 0.57485), (0.49429, 0.60608, -0.62318)-11.65633, -54.35715, 101.17298
2given(-0.9989, 0.03333, 0.03305), (-0.03349, -0.99943, -0.00407), (0.03289, -0.00518, 0.99945)96.55656, 115.93054, -24.49414
3given(0.33066, -0.78699, -0.52088), (-0.80617, 0.05141, -0.58944), (0.49066, 0.61483, -0.61744)110.19384, 169.35269, 77.84708

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Components

#1: Protein
UDP-GALACTOSE 4-EPIMERASE


Mass: 43806.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8T8E9, UDP-glucose 4-epimerase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1285 / 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: 2.6 Å3/Da / Density % sol: 51.7 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLISED WITH NAD AND UDP, FROM 100M HEPES PH7.0, 14% PEG8000, 200MM KCL, pH 7.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlenzyme1drop
25 mMNAD+1drop
35 mMUDP1drop
450 mMTris-HCl1droppH7.5
5100 mMHEPES1reservoirpH7.0
614 %PEG80001reservoir
7200 mM1reservoirKCl
83 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.009
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 112132 / % possible obs: 90.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.09
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.15 / % possible all: 59.3
Reflection
*PLUS
Num. measured all: 417521
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 59.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK6

1ek6


Resolution: 2→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5611 5 %RANDOM
Rwork0.216 ---
obs0.216 112166 89.5 %-
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å20 Å20 Å2
2---4.35 Å20 Å2
3---7.58 Å2
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11411 0 276 1285 12972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.284

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