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- PDB-1gup: STRUCTURE OF NUCLEOTIDYLTRANSFERASE COMPLEXED WITH UDP-GALACTOSE -

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Basic information

Entry
Database: PDB / ID: 1gup
TitleSTRUCTURE OF NUCLEOTIDYLTRANSFERASE COMPLEXED WITH UDP-GALACTOSE
ComponentsGALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
KeywordsNUCLEOTIDYLTRANSFERASE / TRANSFERASE / GALACTOSE METABOLISM
Function / homology
Function and homology information


UDP-glucose-hexose-1-phosphate uridylyltransferase / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / galactokinase activity / galactose catabolic process via UDP-galactose / ferrous iron binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Galactose-1-phosphate uridyl transferase, class I His-active site / Galactose-1-phosphate uridyl transferase family 1 active site signature. / Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily ...Galactose-1-phosphate uridyl transferase, class I His-active site / Galactose-1-phosphate uridyl transferase family 1 active site signature. / Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / GALACTOSE-URIDINE-5'-DIPHOSPHATE / : / Galactose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsThoden, J.B. / Rayment, I. / Holden, H.
CitationJournal: Biochemistry / Year: 1997
Title: Structural analysis of the H166G site-directed mutant of galactose-1-phosphate uridylyltransferase complexed with either UDP-glucose or UDP-galactose: detailed description of the nucleotide sugar binding site.
Authors: Thoden, J.B. / Ruzicka, F.J. / Frey, P.A. / Rayment, I. / Holden, H.M.
History
DepositionOct 23, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
B: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
C: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
D: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,36120
Polymers158,4544
Non-polymers2,90716
Water22,5011249
1
A: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
B: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,68010
Polymers79,2272
Non-polymers1,4538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-73 kcal/mol
Surface area24330 Å2
MethodPISA
2
C: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
D: GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,68010
Polymers79,2272
Non-polymers1,4538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-75 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.700, 57.700, 188.700
Angle α, β, γ (deg.)90.00, 100.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE


Mass: 39613.500 Da / Num. of mol.: 4 / Mutation: H166G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P09148, EC: 2.7.7.10

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Non-polymers , 5 types, 1265 molecules

#2: Chemical
ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1249 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
211-13 %PEG80001drop
350 mMHEPES1drop
4100-150 mM1dropKCl
55 mMUDP-sugar1drop
622-26 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 123 K
DetectorType: BRUKER NONIUS HI-STAR / Detector: MULTIWIRE AREA DETECTOR / Details: SUPER LONG DOUBLE-FOCUSING MIRRORS
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 123193 / % possible obs: 90 %
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. measured all: 244754 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 83 % / Num. unique obs: 13689 / Num. measured obs: 20254 / Rmerge(I) obs: 0.099

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Processing

Software
NameClassification
TNTrefinement
SAINTdata reduction
XCALIBREdata scaling
RefinementResolution: 1.8→30 Å /
RfactorNum. reflection
Rwork0.191 -
obs-120668
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11082 0 156 1249 12487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.38
X-RAY DIFFRACTIONt_dihedral_angle_d16.5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008
X-RAY DIFFRACTIONt_gen_planes0.01
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.5
X-RAY DIFFRACTIONt_planar_d0.008
X-RAY DIFFRACTIONt_plane_restr0.01

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