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- PDB-6pir: Crystal structure of the Legionella effector protein MavE -

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Basic information

Entry
Database: PDB / ID: 6pir
TitleCrystal structure of the Legionella effector protein MavE
ComponentsMavE
KeywordsSIGNALING PROTEIN / Twinned two-helix bundle / NPxY motif / phosphotyrosine binding / membrane-anchored
Function / homologymembrane => GO:0016020 / CITRIC ACID / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsCygler, M. / Voth, K.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)412613 Canada
CitationJournal: To Be Published
Title: Crystal structure of the Legionella effector MavE
Authors: Cygler, M. / Voth, K.A.
History
DepositionJun 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MavE
B: MavE
C: MavE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9035
Polymers47,5193
Non-polymers3842
Water4,540252
1
A: MavE


Theoretical massNumber of molelcules
Total (without water)15,8401
Polymers15,8401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MavE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0322
Polymers15,8401
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MavE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0322
Polymers15,8401
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: MavE

A: MavE


Theoretical massNumber of molelcules
Total (without water)31,6792
Polymers31,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area13720 Å2
MethodPISA
5
C: MavE
hetero molecules

B: MavE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0644
Polymers31,6792
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2280 Å2
ΔGint-17 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.550, 42.050, 46.270
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-275-

HOH

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Components

#1: Protein MavE


Mass: 15839.636 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2344 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZT21
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Citrate, pH 6.0, 18% PEG20K / PH range: 6

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.77 Å / Num. obs: 82310 / % possible obs: 99.3 % / Redundancy: 6.96 % / CC1/2: 0.999 / Net I/σ(I): 15.19
Reflection shellResolution: 1.65→1.69 Å / Num. unique obs: 13055 / CC1/2: 0.593

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→46.267 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.41
RfactorNum. reflection% reflection
Rfree0.2374 2007 5 %
Rwork0.1948 --
obs0.1968 40116 86.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→46.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 26 252 3414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113294
X-RAY DIFFRACTIONf_angle_d1.1514482
X-RAY DIFFRACTIONf_dihedral_angle_d18.3752050
X-RAY DIFFRACTIONf_chiral_restr0.062525
X-RAY DIFFRACTIONf_plane_restr0.007592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.377670.24971279X-RAY DIFFRACTION41
1.6913-1.73710.3915820.32731541X-RAY DIFFRACTION50
1.7371-1.78820.34821010.29611925X-RAY DIFFRACTION61
1.7882-1.84590.30971310.27222489X-RAY DIFFRACTION79
1.8459-1.91190.35471580.28682995X-RAY DIFFRACTION96
1.9119-1.98840.30911580.28053012X-RAY DIFFRACTION96
1.9884-2.07890.23841610.21653056X-RAY DIFFRACTION97
2.0789-2.18850.25771600.19993037X-RAY DIFFRACTION97
2.1885-2.32560.26171620.22163066X-RAY DIFFRACTION97
2.3256-2.50520.23171610.18813063X-RAY DIFFRACTION98
2.5052-2.75730.23681630.18343108X-RAY DIFFRACTION98
2.7573-3.15620.21621650.17993124X-RAY DIFFRACTION98
3.1562-3.97610.21650.16153147X-RAY DIFFRACTION99
3.9761-46.2670.21411730.17253267X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1211-0.03440.47250.6247-0.36581.55930.1322-0.02660.13660.41970.1280.2932-0.66380.0954-0.14920.4844-0.00110.22150.1463-0.01130.34213.698612.745834.6686
21.5406-0.9203-0.23472.02160.04731.99450.0088-0.14660.07280.1619-0.0053-0.1372-0.10110.18920.01270.1533-0.0505-0.04350.1762-0.01620.09933.340727.15639.3061
32.670.68310.06122.28960.11322.6535-0.02850.1048-0.0801-0.10160.016-0.00360.0253-0.02720.01930.12170.0022-0.03080.14580.00060.083533.919419.736516.7786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 36:170 )A36 - 170
2X-RAY DIFFRACTION2( CHAIN B AND RESID 36:172 )B36 - 172
3X-RAY DIFFRACTION3( CHAIN C AND RESID 36:172 )C36 - 172

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