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- PDB-1g3l: THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF... -

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Basic information

Entry
Database: PDB / ID: 1g3l
TitleTHE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-L-RHAMNOSE COMPLEX.
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE / L-RHAMNOSE / NUCLEOTIDYLTRANSFERASE / PYROPHOSPHORYLASE / THYMIDYLYLTRANSFERASE / ALLOSTERY
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region 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
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBlankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naismith, J.H.
Citation
Journal: EMBO J. / Year: 2000
Title: The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
Authors: Blankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The Purification, Crystallisation and Preliminary Structural Characterisation of Glucose-1-Phosphate Thymidylyltransferase (Rmla), the First Enzyme of the Dtdp-L-Rhamnose Synthesis Pathway ...Title: The Purification, Crystallisation and Preliminary Structural Characterisation of Glucose-1-Phosphate Thymidylyltransferase (Rmla), the First Enzyme of the Dtdp-L-Rhamnose Synthesis Pathway from Pseudomonas Aeruginosa
Authors: Blankenfeldt, W. / Giraud, M.F. / Leonard, G. / Rahim, R. / Creuzenet, C. / Lam, J.S. / Naismith, J.H.
#2: Journal: J.Biol.Chem. / Year: 1965
Title: The Nucleotide Specificity and Feedback Control of Thymidine Diphosphate D-Glucose Pyrophosphorylase.
Authors: Melo, A. / Glaser, L.
History
DepositionOct 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)134,82217
Polymers129,9554
Non-polymers4,86713
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21980 Å2
ΔGint-146 kcal/mol
Surface area41590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.087, 138.557, 139.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer consisting of two dimers.

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Components

#1: Protein
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE / GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA)


Mass: 32488.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET23A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(LAMBDA DE3)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H26N2O15P2

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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: 2.55 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 10 % (w/v) PEG 6000, 0.2 M Li-sulfate, 0.1 M Na-citrate pH 4.0; protein incubated with 10 mM dTDP-L-rhamnose, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %(w/v)PEG60001reservoir
20.2 M1reservoirLiSO4
30.1 MNa citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→49.9 Å / Num. obs: 36311 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 37.11 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.8
Reflection shellResolution: 2.8→2.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.9 / % possible all: 70.8
Reflection
*PLUS
Num. measured all: 260832
Reflection shell
*PLUS
% possible obs: 70.8 %

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: 1G1L

1g1l


Resolution: 2.7→100 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.47
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1815 5 %RANDOM
Rwork0.204 ---
obs0.205 34462 93.8 %-
Displacement parametersBiso mean: 12.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--0.01 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9148 0 305 0 9453
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.481.5
X-RAY DIFFRACTIONp_mcangle_it0.8472
X-RAY DIFFRACTIONp_scbond_it1.0973
X-RAY DIFFRACTIONp_scangle_it1.7724.5
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr0.1020.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.39
LS refinement shell
*PLUS
Rfactor Rfree: 0.333 / Rfactor Rwork: 0.255

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