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- PDB-1udb: STRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-4-DEOXY... -

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Basic information

Entry
Database: PDB / ID: 1udb
TitleSTRUCTURE OF UDP-GALACTOSE-4-EPIMERASE COMPLEXED WITH UDP-4-DEOXY-4-FLUORO-ALPHA-D-GLUCOSE
ComponentsUDP-GALACTOSE-4-EPIMERASE
KeywordsISOMERASE / UDP-GALACTOSE / EPIMERASE
Function / homology
Function and homology information


monosaccharide metabolic process / 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, Leloir pathway / galactose metabolic process / NAD+ binding / carbohydrate metabolic process / identical protein binding ...monosaccharide metabolic process / 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, Leloir pathway / galactose metabolic process / NAD+ binding / carbohydrate metabolic process / identical protein binding / cytosol / cytoplasm
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 / DI(HYDROXYETHYL)ETHER / Chem-UFG / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1997
Title: Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli.
Authors: Thoden, J.B. / Hegeman, A.D. / Wesenberg, G. / Chapeau, M.C. / Frey, P.A. / Holden, H.M.
History
DepositionJan 6, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7638
Polymers37,2941
Non-polymers1,4697
Water10,359575
1
A: UDP-GALACTOSE-4-EPIMERASE
hetero molecules

A: UDP-GALACTOSE-4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,52616
Polymers74,5882
Non-polymers2,93814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7860 Å2
ΔGint-88 kcal/mol
Surface area24910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.500, 83.500, 108.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-528-

HOH

31A-594-

HOH

41A-601-

HOH

51A-786-

HOH

61A-973-

HOH

71A-986-

HOH

81A-1042-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-GALACTOSE-4-EPIMERASE / EPIMERASE


Mass: 37294.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P09147, UDP-glucose 4-epimerase

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Non-polymers , 6 types, 582 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-UFG / URIDINE-5'-DIPHOSPHATE-4-DEOXY-4-FLUORO-ALPHA-D-GALACTOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 %PEG80001reservoir
2250-500 mM1reservoirNaCl
350 mMCHES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 49619 / % possible obs: 93 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.65→1.73 Å / Rmerge(I) obs: 0.23 / % possible all: 81
Reflection
*PLUS
Highest resolution: 1.65 Å / Num. measured all: 124280
Reflection shell
*PLUS
% possible obs: 81 % / Num. unique obs: 5317 / Num. measured obs: 8489

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.65→30 Å / Rfactor Rwork: 0.179
Details: SET OF IDEAL BOND LENGTHS AND ANGLES OTHER THAN ENGH AND HUBER USED DURING REFINEMENT
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 94 575 3294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.15
X-RAY DIFFRACTIONt_dihedral_angle_d14.7
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Num. reflection obs: 49616 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.012

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