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- PDB-8hcy: Legionella glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 8hcy
TitleLegionella glycosyltransferase
ComponentsDot/Icm secretion system substrate
KeywordsTRANSFERASE / glucosyltransferase / upd-glucose
Function / homologyGlycosyltransferase family 88 / Glycosyltransferase family 88 / Dot/Icm secretion system substrate
Function and homology information
Biological speciesLegionella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsChen, T.T. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Small Struct / Year: 2023
Title: Structural Basis for the Action Mechanism of Legionella Glycosyltransferase.
Authors: Chen, T.T. / Zheng, S.R. / Tian, L. / Lv, S.L. / Zhong, W.H. / Li, X.L. / Zhang, D.D. / Zheng, X.X. / Ouyang, S.Y.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Dot/Icm secretion system substrate
A: Dot/Icm secretion system substrate
B: Dot/Icm secretion system substrate
D: Dot/Icm secretion system substrate


Theoretical massNumber of molelcules
Total (without water)394,4624
Polymers394,4624
Non-polymers00
Water7,062392
1
C: Dot/Icm secretion system substrate


Theoretical massNumber of molelcules
Total (without water)98,6151
Polymers98,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dot/Icm secretion system substrate


Theoretical massNumber of molelcules
Total (without water)98,6151
Polymers98,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Dot/Icm secretion system substrate


Theoretical massNumber of molelcules
Total (without water)98,6151
Polymers98,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dot/Icm secretion system substrate


Theoretical massNumber of molelcules
Total (without water)98,6151
Polymers98,6151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.361, 112.615, 125.795
Angle α, β, γ (deg.)90.000, 108.143, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Dot/Icm secretion system substrate


Mass: 98615.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella (bacteria) / Gene: C3927_06670 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F8W2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 1.58 Å3/Da / Density % sol: 21.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.64→29.31 Å / Num. obs: 71942 / % possible obs: 95.51 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.23 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.07
Reflection shellResolution: 2.64→2.73 Å / Num. unique obs: 68773 / CC1/2: 0.314

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XGV

7xgv


Resolution: 2.64→29.31 Å / SU ML: 0.2921 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 27.563
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 2001 2.91 %
Rwork0.2396 66773 -
obs0.2401 68774 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.66 Å2
Refinement stepCycle: LAST / Resolution: 2.64→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15824 0 0 392 16216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006816108
X-RAY DIFFRACTIONf_angle_d1.178721764
X-RAY DIFFRACTIONf_chiral_restr0.08162440
X-RAY DIFFRACTIONf_plane_restr0.00572832
X-RAY DIFFRACTIONf_dihedral_angle_d6.80432132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.710.34521330.34524356X-RAY DIFFRACTION87.86
2.71-2.780.3591250.34064441X-RAY DIFFRACTION89.46
2.78-2.860.38131520.32074482X-RAY DIFFRACTION90.47
2.86-2.950.32371200.2944586X-RAY DIFFRACTION92.27
2.95-3.060.27561580.26284656X-RAY DIFFRACTION93.86
3.06-3.180.24611340.24614763X-RAY DIFFRACTION95.27
3.18-3.330.26761370.24464832X-RAY DIFFRACTION97.05
3.33-3.50.23161530.22344874X-RAY DIFFRACTION98.32
3.5-3.720.23821500.20194941X-RAY DIFFRACTION99.01
3.72-4.010.21541480.19684946X-RAY DIFFRACTION99.16
4.01-4.410.20081380.19594964X-RAY DIFFRACTION99.28
4.41-5.040.21381530.19664973X-RAY DIFFRACTION99.59
5.04-6.340.2391500.23785006X-RAY DIFFRACTION99.42
6.34-29.310.2671500.24754953X-RAY DIFFRACTION97.05

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