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- PDB-7x2p: Legionella pneumophila effector RavL -

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Basic information

Entry
Database: PDB / ID: 7x2p
TitleLegionella pneumophila effector RavL
ComponentsPutative lipase
KeywordsHYDROLASE / Legionella pneumophila effector RavL
Function / homology
Function and homology information


O-acyltransferase activity / lipid metabolic process
Similarity search - Function
Lecithin:cholesterol/phospholipid:diacylglycerol acyltransferase / Lecithin:cholesterol acyltransferase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsZheng, J. / Lu, Z. / Chen, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Legionella pneumophila effector RavL
Authors: Zheng, J. / Lu, Z.
History
DepositionFeb 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lipase
B: Putative lipase


Theoretical massNumber of molelcules
Total (without water)57,2682
Polymers57,2682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-2 kcal/mol
Surface area19860 Å2
Unit cell
Length a, b, c (Å)37.377, 54.247, 128.209
Angle α, β, γ (deg.)90.000, 93.610, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 11 through 241)
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUASPA3 - 215
d_21ens_1LEUASPB1 - 213

NCS oper: (Code: givenMatrix: (-0.999374759288, -0.0348474818246, 0.00597858743438), (-0.0332573735659, 0.869104032269, -0.493510008203), (0.0120015665946, -0.49340027777, -0.869719568766)Vector: 19. ...NCS oper: (Code: given
Matrix: (-0.999374759288, -0.0348474818246, 0.00597858743438), (-0.0332573735659, 0.869104032269, -0.493510008203), (0.0120015665946, -0.49340027777, -0.869719568766)
Vector: 19.6652186699, 17.3509898629, 65.1176643753)

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Components

#1: Protein Putative lipase / RavL


Mass: 28634.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1108 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWH7

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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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES sodium pH 7.5, 0.8M potassium tartate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2018
RadiationMonochromator: synchrotron radiation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.89→33.15 Å / Num. obs: 9974 / % possible obs: 85 % / Redundancy: 10 % / Biso Wilson estimate: 43.42 Å2 / CC1/2: 0.84 / Net I/σ(I): 0.1
Reflection shellResolution: 2.89→10 Å / Num. unique obs: 9974 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7a16

7a16


Resolution: 2.89→33.15 Å / SU ML: 0.4466 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3368 989 9.92 %
Rwork0.2842 8985 -
obs0.2893 9974 85.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.99 Å2
Refinement stepCycle: LAST / Resolution: 2.89→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 0 0 3408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063487
X-RAY DIFFRACTIONf_angle_d1.06214717
X-RAY DIFFRACTIONf_chiral_restr0.0708512
X-RAY DIFFRACTIONf_plane_restr0.0073616
X-RAY DIFFRACTIONf_dihedral_angle_d17.7047459
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.75124655513 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.050.3715540.3531533X-RAY DIFFRACTION36.23
3.05-3.240.41851020.3061958X-RAY DIFFRACTION64.87
3.24-3.490.36141730.3221464X-RAY DIFFRACTION98.44
3.49-3.840.3921590.32771501X-RAY DIFFRACTION99.7
3.84-4.390.35261620.25891487X-RAY DIFFRACTION100
4.39-5.530.29271700.25231501X-RAY DIFFRACTION99.82
5.53-33.150.29021690.2681541X-RAY DIFFRACTION99.42
Refinement TLS params.Method: refined / Origin x: 9.78720149515 Å / Origin y: -4.48282342063 Å / Origin z: 33.7573355158 Å
111213212223313233
T0.141211229143 Å20.0823494840109 Å2-0.0051880844615 Å2-0.490702208446 Å2-0.16221078442 Å2--0.0407725287655 Å2
L2.49205704247 °2-0.212741103898 °2-0.0129315736499 °2-1.57269664361 °20.356454464507 °2--1.83003480142 °2
S0.0117237628882 Å °1.69215771577 Å °0.44019330174 Å °-0.391922594267 Å °0.218539734762 Å °-0.00383676591548 Å °-0.0976859512007 Å °0.527702981167 Å °0.107168695233 Å °
Refinement TLS groupSelection details: all

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