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

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Basic information

Entry
Database: PDB / ID: 1fzw
TitleTHE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). APO ENZYME.
ComponentsGLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
KeywordsTRANSFERASE / 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 / extracellular polysaccharide 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
Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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 4, 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_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

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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
E: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,83228
Polymers259,9118
Non-polymers1,92120
Water44,6412478
1
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)130,91614
Polymers129,9554
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint-179 kcal/mol
Surface area43940 Å2
MethodPISA
2
E: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,91614
Polymers129,9554
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14640 Å2
ΔGint-213 kcal/mol
Surface area43530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.656, 73.656, 134.469
Angle α, β, γ (deg.)89.98, 80.91, 80.91
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a tetramer that can be described as a dimer of dimers

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Components

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


Mass: 32488.844 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET23A(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2478 / 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: 2.56 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Na-citrate, 0.5 M Li-sulfate, 9-11% (w/v) PEG 6000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 293 K
Details: Blankenfeldt, W., (2000) Acta Crystallogr.,Sect.D, 56, 1501.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19-12 %(w/v)PEG60001reservoir
20.5 Mlithium sulfate1reservoir
30.1 Mcitrate/NaOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→72.5 Å / Num. all: 202988 / Num. obs: 202988 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.286 / % possible all: 95.6
Reflection
*PLUS
Num. measured all: 377690
Reflection shell
*PLUS
% possible obs: 95.6 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.9→73 Å / SU B: 11.57 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.22 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 10141 5 %RANDOM
Rwork0.176 ---
obs0.18 190758 95.8 %-
Displacement parametersBiso mean: 20.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0.19 Å2-0.13 Å2
2---0.1 Å2-0.09 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18516 0 100 2478 21094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.021
X-RAY DIFFRACTIONp_angle_deg1.869
X-RAY DIFFRACTIONp_mcbond_it2.591.5
X-RAY DIFFRACTIONp_mcangle_it3.522
X-RAY DIFFRACTIONp_scbond_it5.633
X-RAY DIFFRACTIONp_scangle_it6.144.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1650.2
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0.31 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 623 5 %
Rwork-12512 -
obs--93.8 %

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