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- PDB-1ek5: STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+ -

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Basic information

Entry
Database: PDB / ID: 1ek5
TitleSTRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+
ComponentsUDP-GALACTOSE 4-EPIMERASE
KeywordsISOMERASE / Short-Chain Dehydrogenase / Epimerase / Galactosemia
Function / homology
Function and homology information


Defective GALE causes EDG / UDP-N-acetylglucosamine 4-epimerase activity / UDP-N-acetylglucosamine 4-epimerase / galactose catabolic process / Galactose catabolism / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / 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 / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsThoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2000
Title: Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase.
Authors: Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.M.
History
DepositionMar 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-GALACTOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9882
Polymers38,3251
Non-polymers6631
Water3,531196
1
A: UDP-GALACTOSE 4-EPIMERASE
hetero molecules

A: UDP-GALACTOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9764
Polymers76,6492
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)50.300, 116.400, 130.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer constructed from a symmetry partner generated by the two-fold.

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Components

#1: Protein UDP-GALACTOSE 4-EPIMERASE


Mass: 38324.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: FORESKIN / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q14376, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-8000, KCl, HEPPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118-20 %PEG80001reservoir
2100 mMHEPPS1reservoirpH7.5
3250 mM1reservoirKCl
417 mg/mlprotein1drop
52 mMNAD+1drop

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 34184 / Num. obs: 34184 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.258 / Num. unique all: 3761 / % possible all: 87
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 87 % / Num. unique obs: 3761 / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
TNTrefinement
FRAMBOdata collection
SAINTdata scaling
TNTphasing
RefinementResolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3415 -RANDOM
Rwork0.19 ---
all0.191 34184 --
obs0.191 34184 95.2 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 44 196 2915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.36
X-RAY DIFFRACTIONt_bond_d0.011
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.191 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.36
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.6
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.01

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