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- PDB-1iim: thymidylyltransferase complexed with TTP -

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Basic information

Entry
Database: PDB / ID: 1iim
Titlethymidylyltransferase complexed with TTP
Componentsglucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / biosynthetic process / magnesium ion 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-5'-TRIPHOSPHATE / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBarton, W.A. / Lesniak, J. / Biggins, J.B. / Jeffrey, P.D. / Jiang, J. / Rajashankar, K.R. / Thorson, J.S. / Nikolov, D.B.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization.
Authors: Barton, W.A. / Lesniak, J. / Biggins, J.B. / Jeffrey, P.D. / Jiang, J. / Rajashankar, K.R. / Thorson, J.S. / Nikolov, D.B.
History
DepositionApr 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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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)66,8996
Polymers64,9702
Non-polymers1,9294
Water6,936385
1
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)133,79812
Polymers129,9414
Non-polymers3,8578
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area17730 Å2
ΔGint-73 kcal/mol
Surface area40310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.060, 120.060, 94.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second part of the biological assembly is generated by the two fold axis: -x -y -z+1/2

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Components

#1: Protein glucose-1-phosphate thymidylyltransferase / thymidylyltransferase


Mass: 32485.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: LT2 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q9F7K6, UniProt: P26393*PLUS, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris, Mono-ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mM1dropKCl
32 mM1dropMgCl2
410 mMHEPES1drop
52.0 Mammonium phosphate1reservoir
60.1 MTris-HCl1reservoir
720 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→19.26 Å / Num. all: 45400 / Observed criterion σ(F): 0 / Biso Wilson estimate: 18.8 Å2 / Limit h max: 59 / Limit h min: 0 / Limit k max: 40 / Limit k min: 0 / Limit l max: 46 / Limit l min: 0 / Observed criterion F max: 299778.95 / Observed criterion F min: 0.32
Reflection
*PLUS
% possible obs: 98.2 % / Redundancy: 9 % / Rmerge(I) obs: 0.109

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 2.1→19.26 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
Details: There are three C-terminal residues in the crystal for which the author does not see clear density: LYS 290, GLY 291, LEU 292. There is no density beyond the CB for LYS 154.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3893 10 %random
Rwork0.198 ---
all-40746 --
obs-39043 95.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 52.2732 Å2 / ksol: 0.369264 e/Å3
Displacement parametersBiso max: 59.32 Å2 / Biso mean: 23.92 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.22 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.1→19.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 116 385 5015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_torsion_deg22.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.20.2694408.80.26841630.0135007460391.9
2.2-2.310.24945590.24942240.0125047467992.7
2.31-2.460.2234869.70.22343350.015011482196.2
2.46-2.640.2084959.80.20844250.0095038492097.7
2.64-2.910.213509100.21344580.0095065496798
2.91-3.330.21351910.20.21344960.0095102501598.3
3.33-4.190.1814989.70.18243670.0085139486594.6
4.19-19.260.1934919.10.19246820.0095370517396.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ttp.parttp.top
X-RAY DIFFRACTION4water_rep.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 45403 / Num. reflection Rfree: 3583 / % reflection Rfree: 10 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.269 / % reflection Rfree: 8.8 % / Rfactor Rwork: 0.268

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