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- PDB-4ho2: Crystal structure of glucose 1-phosphate thymidylyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 4ho2
TitleCrystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine
ComponentsGlucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / thymidylyltransferase / nucleotide binding
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / biosynthetic process / nucleotide binding / metal ion binding
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 / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesAneurinibacillus thermoaerophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsChen, T.J. / Chien, W.T. / Lin, C.C. / Wang, W.C.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine
Authors: Chen, T.J. / Chien, W.T. / Lin, C.C. / Wang, W.C.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7466
Polymers32,9741
Non-polymers7735
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,98524
Polymers131,8954
Non-polymers3,09120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area18840 Å2
ΔGint-246 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.895, 91.895, 70.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-524-

HOH

31A-567-

HOH

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Components

#1: Protein Glucose-1-phosphate thymidylyltransferase


Mass: 32973.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aneurinibacillus thermoaerophilus (bacteria)
Gene: rmlA / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9AGY4, glucose-1-phosphate thymidylyltransferase
#2: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 2.0M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2011 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. all: 26525 / Num. obs: 26483 / % possible obs: 99.5 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 13 % / Rmerge(I) obs: 0.357 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H5R

1h5r


Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.919 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1334 5 %RANDOM
Rwork0.1934 ---
obs0.1954 26483 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.33 Å2 / Biso mean: 30.1519 Å2 / Biso min: 16.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 49 186 2491
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.019
X-RAY DIFFRACTIONr_angle_refined_deg1.568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.23
X-RAY DIFFRACTIONr_chiral_restr0.17
X-RAY DIFFRACTIONr_gen_planes_refined0.013
X-RAY DIFFRACTIONr_mcbond_it1.437
X-RAY DIFFRACTIONr_mcangle_it2.358
X-RAY DIFFRACTIONr_scbond_it
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 95 -
Rwork0.207 1815 -
all-1910 -
obs--99.79 %

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