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- PDB-4ho9: Crystal structure of glucose 1-phosphate thymidylyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 4ho9
TitleCrystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP
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
GALACTOSE-URIDINE-5'-DIPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesAneurinibacillus thermoaerophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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-galactose and UTP
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,91315
Polymers65,9472
Non-polymers2,96513
Water9,386521
1
A: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5048
Polymers32,9741
Non-polymers1,5317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4087
Polymers32,9741
Non-polymers1,4356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,82630
Polymers131,8954
Non-polymers5,93126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area22590 Å2
ΔGint-307 kcal/mol
Surface area42350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.788, 90.763, 87.702
Angle α, β, γ (deg.)90.000, 125.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glucose-1-phosphate thymidylyltransferase


Mass: 32973.664 Da / Num. of mol.: 2
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-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 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: 1.8→30 Å / Num. obs: 67790 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.042 / Χ2: 1.042 / Net I/σ(I): 22.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.864.10.21467761.009199.7
1.86-1.944.20.1567751.062199.8
1.94-2.034.20.10167781.079199.9
2.03-2.134.20.07867631.059199.9
2.13-2.274.20.06167391.096199.8
2.27-2.444.20.05468251.005199.9
2.44-2.694.20.04267771.0311100
2.69-3.084.10.03968060.972199.9
3.08-3.883.90.0467951.09199.4
3.88-303.90.02967561.014197.8

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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: 1.8→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.102 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 3441 5.1 %RANDOM
Rwork0.1714 ---
obs0.1734 67775 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.16 Å2 / Biso mean: 25.9325 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-1.16 Å2
2--1.15 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 175 521 5253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224815
X-RAY DIFFRACTIONr_angle_refined_deg1.4552.036539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12324.581203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2361524
X-RAY DIFFRACTIONr_chiral_restr0.1310.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213502
X-RAY DIFFRACTIONr_mcbond_it1.6451.52878
X-RAY DIFFRACTIONr_mcangle_it2.70824630
X-RAY DIFFRACTIONr_scbond_it4.28731937
X-RAY DIFFRACTIONr_scangle_it6.8054.51909
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 246 -
Rwork0.217 4761 -
all-5007 -
obs--99.66 %

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