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- PDB-1h5t: Thymidylyltransferase complexed with Thymidylyldiphosphate-glucose -

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Basic information

Entry
Database: PDB / ID: 1h5t
TitleThymidylyltransferase complexed with Thymidylyldiphosphate-glucose
Components(Glucose-1-phosphate thymidylyltransferase ...) x 2
KeywordsTRANSFERASE / PYROPHOSPHATASE / NUCLEOTIDE SUGAR METHABOLISM
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / protein homotetramerization / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Glucose-1-phosphate thymidylyltransferase, short form / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / THYMIDINE-5'-DIPHOSPHATE / Glucose-1-phosphate thymidylyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRosano, C. / Zuccotti, S. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Kinetic and Crystallographic Analyses Support a Sequential-Ordered Bi Bi Catalytic Mechanism for Escherichia Coli Glucose-1-Phosphate Thymidylyltransferase
Authors: Zuccotti, S. / Zanardi, D. / Rosano, C. / Sturla, L. / Tonetti, M. / Bolognesi, M.
History
DepositionMay 25, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 5, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-1-phosphate thymidylyltransferase 1
B: Glucose-1-phosphate thymidylyltransferase 1
C: Glucose-1-phosphate thymidylyltransferase 1
D: Glucose-1-phosphate thymidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,84713
Polymers130,8854
Non-polymers3,9629
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.810, 119.490, 81.170
Angle α, β, γ (deg.)90.00, 112.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Glucose-1-phosphate thymidylyltransferase ... , 2 types, 4 molecules ACDB

#1: Protein Glucose-1-phosphate thymidylyltransferase 1 / / G1P-TT 1 / dTDP-glucose pyrophosphorylase 1 / dTDP-glucose synthase 1


Mass: 32726.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfbA, rmlA, rmlA1, b2039, JW2024 / Production host: Escherichia coli (E. coli)
References: UniProt: P37744, glucose-1-phosphate thymidylyltransferase
#2: Protein Glucose-1-phosphate thymidylyltransferase 1 / / G1P-TT 1 / dTDP-glucose pyrophosphorylase 1 / dTDP-glucose synthase 1


Mass: 32705.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfbA, rmlA, rmlA1, b2039, JW2024 / Production host: Escherichia coli (E. coli)
References: UniProt: P37744, glucose-1-phosphate thymidylyltransferase

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Non-polymers , 4 types, 510 molecules

#3: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical
ChemComp-DAU / 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / Thymidine diphosphate glucose


Mass: 564.329 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growpH: 5.5 / Details: pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 98078 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→12 Å / SU ML: 0.1019 / ESU R Free: 0.1449 / Details: PROLINE 19 IS IN CIS CONFORMATION
RfactorNum. reflection% reflectionSelection details
Rfree0.224 --RANDOM
Rwork0.174 ---
obs-92823 97.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9089 0 249 501 9839

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