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- PDB-1iin: thymidylyltransferase complexed with UDP-glucose -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1iin
Titlethymidylyltransferase complexed with UDP-glucose
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
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucose-1-phosphate thymidylyltransferase / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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: 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
C: glucose-1-phosphate thymidylyltransferase
D: glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2068
Polymers129,9414
Non-polymers2,2654
Water13,727762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13760 Å2
ΔGint-70 kcal/mol
Surface area42770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.900, 112.141, 132.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32485.201 Da / Num. of mol.: 4
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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium Sulfate, iso-propanol, pH 7, 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
51.9 Mammonium sulfate1reservoir
67.5 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 Å
DetectorType: CUSTOM-MADE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→39.83 Å / Num. all: 93944 / Observed criterion σ(F): 0 / Biso Wilson estimate: 9.7 Å2 / Limit h max: 46 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 66 / Limit l min: 0 / Observed criterion F max: 127108.29 / Observed criterion F min: 0.32
Reflection
*PLUS
% possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→39.83 Å / Rfactor Rfree error: 0.002 / 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
Rfree0.224 8054 10 %random
Rwork0.184 ---
all-81193 --
obs-80491 99.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 55.0659 Å2 / ksol: 0.371202 e/Å3
Displacement parametersBiso max: 72.5 Å2 / Biso mean: 20.26 Å2 / Biso min: 2.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2--1.28 Å20 Å2
3---0.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.1→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9028 0 144 762 9934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_torsion_deg23.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.95
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 (%)
2.1-2.20.25039859.80.194588270.00610040981297.7
2.2-2.310.1869949.90.18689030.00610064989798.3
2.31-2.460.182102210.20.18289100.00610060993298.7
2.46-2.650.1899859.80.18990030.00610095998898.9
2.65-2.910.1969609.50.19690470.006100761000799.3
2.91-3.330.195103210.10.19591030.006101701013599.7
3.33-4.20.1761025100.17791650.005102091019099.8
4.2-39.830.1951051100.19494790.006105541053099.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3udp.parudp.top
X-RAY DIFFRACTION4water_rep.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 179416 / Num. reflection Rfree: 2276 / % reflection Rfree: 10 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.74
LS refinement shell
*PLUS
% reflection Rfree: 9.8 %

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