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- PDB-5jg4: Structure of the effector protein LpiR1 (Lpg0634) from Legionella... -

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Basic information

Entry
Database: PDB / ID: 5jg4
TitleStructure of the effector protein LpiR1 (Lpg0634) from Legionella pneumophila
Componentseffector protein LpiR1
KeywordsSIGNALING PROTEIN / Legionella pneumophila / bacterial effector / phosphate binding
Function / homologyCITRATE ANION / PHOSPHATE ION / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBeyrakhova, K. / van Straaten, K. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Investigations of the Effector Protein LpiR1 from Legionella pneumophila.
Authors: Beyrakhova, K.A. / van Straaten, K. / Li, L. / Boniecki, M.T. / Anderson, D.H. / Cygler, M.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: effector protein LpiR1
B: effector protein LpiR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9319
Polymers101,0832
Non-polymers8477
Water4,071226
1
A: effector protein LpiR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0135
Polymers50,5421
Non-polymers4714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: effector protein LpiR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9184
Polymers50,5421
Non-polymers3763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.840, 96.240, 151.450
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 effector protein LpiR1


Mass: 50541.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpymg_00644 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C9P234
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M citrate pH 4.0, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 48632 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.529 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.92
RfactorNum. reflection% reflection
Rfree0.225 2432 5 %
Rwork0.1865 --
obs0.1884 48632 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6023 0 53 226 6302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036156
X-RAY DIFFRACTIONf_angle_d0.5278322
X-RAY DIFFRACTIONf_dihedral_angle_d15.2983796
X-RAY DIFFRACTIONf_chiral_restr0.038982
X-RAY DIFFRACTIONf_plane_restr0.0031070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4490.25991400.2252665X-RAY DIFFRACTION100
2.449-2.50230.25591400.20632672X-RAY DIFFRACTION100
2.5023-2.56050.26461420.21142689X-RAY DIFFRACTION100
2.5605-2.62450.22881420.21232688X-RAY DIFFRACTION100
2.6245-2.69540.2561410.21052683X-RAY DIFFRACTION100
2.6954-2.77470.2451400.19732675X-RAY DIFFRACTION100
2.7747-2.86430.26091420.19022681X-RAY DIFFRACTION100
2.8643-2.96670.22151410.20452695X-RAY DIFFRACTION100
2.9667-3.08540.27071430.20592718X-RAY DIFFRACTION100
3.0854-3.22580.24091430.18772709X-RAY DIFFRACTION100
3.2258-3.39580.1981420.18862692X-RAY DIFFRACTION100
3.3958-3.60850.20141430.18812720X-RAY DIFFRACTION100
3.6085-3.88710.24421440.17342729X-RAY DIFFRACTION100
3.8871-4.2780.19781430.15772728X-RAY DIFFRACTION100
4.278-4.89650.17621460.1562761X-RAY DIFFRACTION100
4.8965-6.16710.26351460.20172781X-RAY DIFFRACTION100
6.1671-48.53870.20921540.18462914X-RAY DIFFRACTION100

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