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- PDB-1nai: UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED -

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Basic information

Entry
Database: PDB / ID: 1nai
TitleUDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED
ComponentsUDP-GALACTOSE 4-EPIMERASE
KeywordsISOMERASE
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 / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsThoden, J.B. / Frey, P.A. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1996
Title: Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli.
Authors: Thoden, J.B. / Frey, P.A. / Holden, H.M.
History
DepositionNov 22, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: 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 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr1_symmetry / _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)38,5907
Polymers37,2941
Non-polymers1,2966
Water6,449358
1
A: UDP-GALACTOSE 4-EPIMERASE
hetero molecules

A: UDP-GALACTOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,18014
Polymers74,5882
Non-polymers2,59212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6980 Å2
ΔGint-58 kcal/mol
Surface area25280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.500, 83.500, 108.200
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-513-

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 genetically manipulated source
Details: OXIDIZED FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7E2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), PLYSS / References: UniProt: P09147, UDP-glucose 4-epimerase

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Non-polymers , 6 types, 364 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / 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-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mg/mlenzyme1drop
25 mMUDP1drop
315 %PEG80001drop
4500 mM1dropNaCl
550 mMHEPES1drop
615 %PEG1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 39504 / % possible obs: 96 %
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. measured all: 63946 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 93 % / Num. unique obs: 7122 / Num. measured obs: 9216 / Rmerge(I) obs: 0.225

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2→30 Å / Details: TNT /
RfactorNum. reflection
Rwork0.193 -
obs-29318
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 83 358 3066
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d15.6
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.007
X-RAY DIFFRACTIONt_gen_planes0.012
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.6
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.012

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