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- PDB-1ek6: STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH NADH ... -

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Basic information

Entry
Database: PDB / ID: 1ek6
TitleSTRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH NADH AND UDP-GLUCOSE
ComponentsUDP-GALACTOSE 4-EPIMERASE
KeywordsISOMERASE / Epimerase / Short-Chain Dehydrogenase / Galactosemia
Function / homology
Function and homology information


Defective GALE causes EDG / UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / galactose catabolic process / Galactose catabolism / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / TETRAMETHYLAMMONIUM ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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.name
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,38411
Polymers76,6492
Non-polymers2,7359
Water16,195899
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-39 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.700, 86.900, 95.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailshomodimer constructed from chains A & B

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-GALACTOSE 4-EPIMERASE


Mass: 38324.605 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 908 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Chemical ChemComp-TMA / TETRAMETHYLAMMONIUM ION


Mass: 74.145 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 273 K / Method: batch / pH: 6
Details: PEG 3400, magnesium chloride, MES, NADH, UDP-glucose, sodium chloride, pH 6.0, BATCH, temperature 273.0K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES11pH6.0
28.5 %PEG340012
375 mM12MgCl2
41
51

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7
DetectorType: SBC-2 / Detector: CCD / Date: Dec 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 96156 / Num. obs: 96156 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.286 / Num. unique all: 8401 / % possible all: 84.7
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 84.7 % / Num. unique obs: 8401 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
MADNESSdata reduction
HKL-2000data scaling
RefinementResolution: 1.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 9611 -RANDOM
Rwork0.168 ---
all0.169 96156 --
obs0.169 96156 96.1 %-
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 177 899 6489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.04
X-RAY DIFFRACTIONt_bond_d0.01
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 96012 / σ(F): 0 / Rfactor all: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.04
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.011
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.7

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