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- PDB-4ho8: Crystal structure of glucose 1-phosphate thymidylyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 4ho8
TitleCrystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-glucose and 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 / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesAneurinibacillus thermoaerophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 UDP-glucose and 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 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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
B: Glucose-1-phosphate thymidylyltransferase
C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,47426
Polymers131,8954
Non-polymers4,57922
Water2,810156
1
A: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0706
Polymers32,9741
Non-polymers1,0975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1667
Polymers32,9741
Non-polymers1,1936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1667
Polymers32,9741
Non-polymers1,1936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0706
Polymers32,9741
Non-polymers1,0975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21740 Å2
ΔGint-306 kcal/mol
Surface area40700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.016, 91.250, 91.233
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glucose-1-phosphate thymidylyltransferase


Mass: 32973.664 Da / Num. of mol.: 4
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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 1.8M 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: Aug 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: 2.6→30 Å / Num. obs: 35282 / % possible obs: 98.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.045 / Χ2: 1.049 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.693.20.40435231.052198.8
2.69-2.83.20.26334821.059198.8
2.8-2.933.20.19435251.064199.2
2.93-3.083.20.12935341.058199
3.08-3.283.20.07835271.084199.4
3.28-3.533.20.05235411.058199.4
3.53-3.883.20.04235301.028199.2
3.88-4.443.20.03235991.061199.3
4.44-5.593.20.02635440.993199.6
5.59-303.10.02334771.029194.8

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Processing

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

1h5r


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.737 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 1741 4.9 %RANDOM
Rwork0.1854 ---
obs0.1882 35267 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 127.75 Å2 / Biso mean: 49.2988 Å2 / Biso min: 22.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.83 Å2
2---0.4 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9024 0 282 156 9462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229476
X-RAY DIFFRACTIONr_angle_refined_deg1.2662.02212848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.06451148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23224.554404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.576151644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3961548
X-RAY DIFFRACTIONr_chiral_restr0.0990.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216952
X-RAY DIFFRACTIONr_mcbond_it0.7851.55696
X-RAY DIFFRACTIONr_mcangle_it1.52929160
X-RAY DIFFRACTIONr_scbond_it2.25433780
X-RAY DIFFRACTIONr_scangle_it3.7094.53688
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 103 -
Rwork0.255 2369 -
all-2472 -
obs--94.39 %

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