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- PDB-1h5s: Thymidylyltransferase complexed with TMP -

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Basic information

Entry
Database: PDB / ID: 1h5s
TitleThymidylyltransferase complexed with TMP
Components(Glucose-1-phosphate thymidylyltransferase ...) x 4
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 / protein homotetramerization / metal ion binding / identical protein 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
THYMIDINE-5'-PHOSPHATE / Glucose-1-phosphate thymidylyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Nov 28, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / 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 / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_site / _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
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)133,42512
Polymers130,8484
Non-polymers2,5788
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.100, 119.270, 81.110
Angle α, β, γ (deg.)90.00, 112.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Glucose-1-phosphate thymidylyltransferase ... , 4 types, 4 molecules ABCD

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


Mass: 32693.457 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
#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
#3: Protein Glucose-1-phosphate thymidylyltransferase 1 / G1P-TT 1 / dTDP-glucose pyrophosphorylase 1 / dTDP-glucose synthase 1


Mass: 32726.465 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
#4: Protein Glucose-1-phosphate thymidylyltransferase 1 / G1P-TT 1 / dTDP-glucose pyrophosphorylase 1 / dTDP-glucose synthase 1


Mass: 32722.453 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 , 2 types, 400 molecules

#5: Chemical
ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N2O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.91
DetectorDate: Jul 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 56185 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.1

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→12 Å / SU ML: 0.1836 / ESU R Free: 0.3327 / Details: PROLINE 19 IS IN CIS CONFORMATION
RfactorNum. reflection% reflectionSelection details
Rfree0.257 --RANDOM
Rwork0.176 ---
obs-53169 99 %-
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9107 0 168 392 9667

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