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- PDB-1a9z: UDP-GALACTOSE 4-EPIMERASE MUTANT S124A/Y149F COMPLEXED WITH UDP-G... -

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Basic information

Entry
Database: PDB / ID: 1a9z
TitleUDP-GALACTOSE 4-EPIMERASE MUTANT S124A/Y149F COMPLEXED WITH UDP-GALACTOSE
ComponentsUDP-GALACTOSE 4-EPIMERASE
KeywordsEPIMERASE / GALACTOSE METABOLISM / DEHYDROGENASE
Function / homology
Function and homology information


colanic acid biosynthetic process / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / racemase and epimerase activity, acting on carbohydrates and derivatives / galactose catabolic process via UDP-galactose / 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 / TRIETHYLENE GLYCOL / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER DIFFERENCE / Resolution: 1.9 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1998
Title: Dramatic differences in the binding of UDP-galactose and UDP-glucose to UDP-galactose 4-epimerase from Escherichia coli.
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionApr 14, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Nov 3, 2021Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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
Revision 2.1Feb 7, 2024Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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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)38,7117
Polymers37,2621
Non-polymers1,4496
Water9,746541
1
A: UDP-GALACTOSE 4-EPIMERASE
hetero molecules

A: UDP-GALACTOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,42214
Polymers74,5242
Non-polymers2,89812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7280 Å2
ΔGint-89 kcal/mol
Surface area25400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.900, 83.900, 108.100
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-445-

HOH

21A-494-

HOH

31A-502-

HOH

41A-719-

HOH

51A-853-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-GALACTOSE 4-EPIMERASE


Mass: 37262.016 Da / Num. of mol.: 1 / Mutation: S124A, Y149F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P09147, UDP-glucose 4-epimerase

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Non-polymers , 5 types, 547 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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsNAD IS THE COFACTOR UDP IS THE SUBSTRATE

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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: 59 %
Crystal growpH: 9
Details: CRYSTALLIZED FROM 18% PEG8000, 500MM NACL, 20MM UDP-GALACTOSE THEN SOAKED IN 25% PEG8000, 750MM NACL, 20MM UDP-GALACTOSE, 20% ETHYLENE GLYCOL, pH 9.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 mg/mlprotein1drop
218-25 %(w/v)PEG80001reservoir
3400-800 mM1reservoirNaCl
450 mMCHES1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 1, 1998 / Details: GOEBEL FOCUSING OPTICS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 32710 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 24.6
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.228 / % possible all: 74
Reflection
*PLUS
Num. measured all: 112562
Reflection shell
*PLUS
% possible obs: 74 % / Num. unique obs: 3288 / Num. measured obs: 5712

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Processing

Software
NameVersionClassification
TNT5Erefinement
SAINTdata reduction
XCALIBREdata scaling
RefinementMethod to determine structure: FOURIER DIFFERENCE / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.188 --
all0.188 32710 -
obs0.188 32710 91 %
Rfree-0 -
Solvent computationSolvent model: TNT / Bsol: 906.6 Å2 / ksol: 1.236 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 93 541 3257
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00741365
X-RAY DIFFRACTIONt_angle_deg2.52654583
X-RAY DIFFRACTIONt_dihedral_angle_d15.04825880
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006748
X-RAY DIFFRACTIONt_gen_planes0.01373710
X-RAY DIFFRACTIONt_it032570
X-RAY DIFFRACTIONt_nbd0.079613
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.0480
X-RAY DIFFRACTIONt_planar_d0.0068
X-RAY DIFFRACTIONt_plane_restr0.01310

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