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- PDB-2cnb: Trypanosoma brucei UDP-galactose-4-epimerase in ternary complex w... -

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Basic information

Entry
Database: PDB / ID: 2cnb
TitleTrypanosoma brucei UDP-galactose-4-epimerase in ternary complex with NAD and the substrate analogue UDP-4-deoxy-4-fluoro-alpha-D-galactose
ComponentsUDP-GALACTOSE-4-EPIMERASE
KeywordsEPIMERASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / UDP-GALACTOSE-4- EPIMERASE / NAD / ISOMERASE / TRYPANOSOMA BRUCEI / UDP-4-DEOXY- 4-FLUORO-ALPHA-D-GALACTOSE
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / glycosome / nucleotide binding
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 / Chem-UFG / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.7 Å
AuthorsAlphey, M.S. / Ferguson, M.A.J. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Trypanosoma Brucei Udp-Galactose-4-Epimerase in Ternary Complex with Nad+ and the Substrate Analogue Udp-4-Deoxy-4-Fluoro-Alpha-D-Galactose
Authors: Alphey, M.S. / Burton, A. / Urbaniak, M. / Boons, G.J. / Ferguson, M.A.J. / Hunter, W.N.
History
DepositionMay 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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)180,15312
Polymers175,2264
Non-polymers4,9278
Water7,494416
1
A: UDP-GALACTOSE-4-EPIMERASE
B: UDP-GALACTOSE-4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0776
Polymers87,6132
Non-polymers2,4634
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)90,0776
Polymers87,6132
Non-polymers2,4634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.724, 111.694, 160.873
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(-0.3229, 0.8009, 0.5043), (0.7888, -0.06665, 0.611), (0.523, 0.5951, -0.6102)-7.992, -57.25, 98.81
2given(-0.9985, -0.04752, 0.02796), (0.04747, -0.9989, -0.00274), (0.02806, -0.001409, 0.9996)101.7, 111, 21.84
3given(0.351, -0.7873, 0.5069), (-0.7775, 0.05667, 0.6264), (-0.5219, -0.6139, -0.5922)58.63, 28.39, 204.3

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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-UFG / URIDINE-5'-DIPHOSPHATE-4-DEOXY-4-FLUORO-ALPHA-D-GALACTOSE


Mass: 568.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER -1 AND HIS 0 IN EACH SUBUNIT CORRESPOND TO A VISIBLE FRAGMENT OF THE 6HIS AFFINITY TAG USED FOR ...SER -1 AND HIS 0 IN EACH SUBUNIT CORRESPOND TO A VISIBLE FRAGMENT OF THE 6HIS AFFINITY TAG USED FOR PURIFICATION

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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: 3 Å3/Da / Density % sol: 58.7 %
Crystal growpH: 8
Details: 8% PEG 8000, 200MM KCL, 50MM NA2B4O7, 5% GLYCEROL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 11, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→92 Å / Num. obs: 49501 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 64.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→91.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.906 / SU B: 15.525 / SU ML: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2454 5.05 %RANDOM
Rwork0.199 ---
obs0.203 48640 95.3 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.29 Å2
Baniso -1Baniso -2Baniso -3
1-3.481 Å20 Å20 Å2
2--0.428 Å20 Å2
3----3.909 Å2
Refinement stepCycle: LAST / Resolution: 2.7→91.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11348 0 320 416 12084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.99216409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20651477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01223.063542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6171598
X-RAY DIFFRACTIONr_chiral_restr0.0990.21803
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.26045
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.28051
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.57444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.135211752
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.43935159
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2664.54644
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 11.98→91.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 21
Rwork0.224 466

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