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- PDB-3jsz: Legionella pneumophila glucosyltransferase Lgt1 N293A with UDP-Glc -

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Basic information

Entry
Database: PDB / ID: 3jsz
TitleLegionella pneumophila glucosyltransferase Lgt1 N293A with UDP-Glc
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / glucosyltransferase / Legionnaire's disease / Legionella pneumophila
Function / homology
Function and homology information


Rna Polymerase Sigma Factor; Chain: A - #130 / Glycosyltransferase family 88, C-terminal domain / Glycosyltransferase family 88 / Glycosyltransferase family 88 / Rna Polymerase Sigma Factor; Chain: A / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucosyltransferase Lgt1
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsLu, W. / Du, J. / Belyi, Y. / Stahl, M. / Zivilikidis, T. / Gerhardt, S. / Aktories, K. / Einsle, O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural Basis of the Action of Glucosyltransferase Lgt1 from Legionella pneumophila.
Authors: Lu, W. / Du, J. / Stahl, M. / Tzivelekidis, T. / Belyi, Y. / Gerhardt, S. / Aktories, K. / Einsle, O.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6913
Polymers60,1001
Non-polymers5912
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.232, 122.232, 102.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Putative uncharacterized protein / Lgt1


Mass: 60100.418 Da / Num. of mol.: 1 / Mutation: N293A / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / Strain: Lens / References: UniProt: Q5WWY0
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 293.15 K / pH: 5
Details: 23% PEG3350, 0.06M ammonium acetat, 0.1M sodium acetate buffer, pH5.0, temperature 293.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00, 0.97973, 0.97957, 0.97205
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979731
30.979571
40.972051
ReflectionResolution: 1.7→22 Å / Num. obs: 62915 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.9 / Num. unique all: 60773 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0072 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→21.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.903 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19318 3192 5.1 %RANDOM
Rwork0.1656 ---
obs0.16701 59723 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.846 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 37 712 4884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224325
X-RAY DIFFRACTIONr_bond_other_d0.0010.022961
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9745876
X-RAY DIFFRACTIONr_angle_other_deg0.83137259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3975536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54724.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05815759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3111522
X-RAY DIFFRACTIONr_chiral_restr0.0650.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.621.52631
X-RAY DIFFRACTIONr_mcbond_other0.1251.51051
X-RAY DIFFRACTIONr_mcangle_it1.20924268
X-RAY DIFFRACTIONr_scbond_it2.06131694
X-RAY DIFFRACTIONr_scangle_it3.2444.51600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 231 -
Rwork0.196 4374 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 32.6081 Å / Origin y: 4.4195 Å / Origin z: 1.2796 Å
111213212223313233
T0.0125 Å2-0.0001 Å2-0.0052 Å2-0.0112 Å2-0.0009 Å2--0.0049 Å2
L0.1339 °20.0739 °2-0.0108 °2-0.4252 °2-0.0058 °2--0.0889 °2
S0.0081 Å °-0.0143 Å °-0.0112 Å °0.0072 Å °0.0068 Å °-0.0008 Å °0.0026 Å °0.011 Å °-0.0149 Å °

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