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- PDB-1h5r: Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1h5r
TitleThymidylyltransferase complexed with Thimidine and Glucose-1-phospate
Components(GLUCOSE-1-PHOSPHATE ...) 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 / 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
1-O-phosphono-alpha-D-glucopyranose / THYMIDINE / 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 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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
B: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,34321
Polymers130,8854
Non-polymers3,45917
Water8,521473
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, 118.960, 80.590
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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GLUCOSE-1-PHOSPHATE ... , 2 types, 4 molecules ACDB

#1: Protein GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE / TDP-GLUCOSE SYNTHASE / DTDP-GLUCOSE PYROPHOSPHORYLASE


Mass: 32726.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P37744, glucose-1-phosphate thymidylyltransferase
#2: Protein GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE / TDP-GLUCOSE SYNTHASE / DTDP-GLUCOSE PYROPHOSPHORYLASE


Mass: 32705.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P37744, glucose-1-phosphate thymidylyltransferase

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 486 molecules

#3: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N2O5
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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
Crystal grow
*PLUS
pH: 5.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
25 mMdeoxythymidine1drop
35 mMG1P1drop
41.7 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoirpH5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.936
DetectorDate: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 99207 / % possible obs: 85.4 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 586259

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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: 0.1297 / ESU R Free: 0.1716 / Details: PROLINE 19 IS IN CIS CONFORMATION
RfactorNum. reflection% reflectionSelection details
Rfree0.234 --RANDOM
Rwork0.173 ---
obs-80205 85.37 %-
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9093 0 225 473 9791
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.945
X-RAY DIFFRACTIONp_plane_restr0.02

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