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- PDB-6wo6: Structure of RavA (lpp0008) E38A/K39A surface entropy reduction mutant -

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Basic information

Entry
Database: PDB / ID: 6wo6
TitleStructure of RavA (lpp0008) E38A/K39A surface entropy reduction mutant
ComponentsRavA
KeywordsCELL INVASION / Legionella pneumophila Effector
Function / homologyUncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila str. Paris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsCygler, M. / Chung, I.Y.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Protein Sci. / Year: 2021
Title: Structural and functional study of Legionella pneumophila effector RavA.
Authors: Chung, I.Y.W. / Li, L. / Tyurin, O. / Gagarinova, A. / Wibawa, R. / Li, P. / Hartland, E.L. / Cygler, M.
History
DepositionApr 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: RavA
B: RavA


Theoretical massNumber of molelcules
Total (without water)74,5782
Polymers74,5782
Non-polymers00
Water64936
1
A: RavA


Theoretical massNumber of molelcules
Total (without water)37,2891
Polymers37,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RavA


Theoretical massNumber of molelcules
Total (without water)37,2891
Polymers37,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.460, 62.670, 286.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11B-413-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 1 through 25 or (resid 26...A1 - 327
211(chain 'B' and (resid 1 through 15 or (resid 16...B1 - 327

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Components

#1: Protein RavA


Mass: 37289.211 Da / Num. of mol.: 2 / Mutation: E38A/K39A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila str. Paris (bacteria)
Gene: D1H98_04490 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A6VZ03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 8000 and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→47.82 Å / Num. obs: 22566 / % possible obs: 94.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 63.55 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.96
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 3.82 % / Num. unique obs: 1679 / CC1/2: 0.835 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→47.82 Å / SU ML: 0.3471 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.2982
RfactorNum. reflection% reflection
Rfree0.23 1129 5.01 %
Rwork0.2025 --
obs0.2039 22555 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.59 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 0 36 5106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295154
X-RAY DIFFRACTIONf_angle_d0.53486974
X-RAY DIFFRACTIONf_chiral_restr0.0385799
X-RAY DIFFRACTIONf_plane_restr0.0031933
X-RAY DIFFRACTIONf_dihedral_angle_d22.46911892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.35611400.30342660X-RAY DIFFRACTION96.49
2.93-3.080.35071420.26912689X-RAY DIFFRACTION96.23
3.08-3.270.31821400.26212663X-RAY DIFFRACTION95.93
3.27-3.530.30251410.24662674X-RAY DIFFRACTION95.65
3.53-3.880.22631410.20282677X-RAY DIFFRACTION95.17
3.88-4.440.2011390.17242638X-RAY DIFFRACTION93.69
4.44-5.60.18951400.17742671X-RAY DIFFRACTION93.11
5.6-47.820.18241460.17392754X-RAY DIFFRACTION90.48
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)
15.28843137085-2.07943625839-2.208391944232.32723556591.186660254594.67727256190.1902383586130.5712285963470.135754570718-0.118781821189-0.00618725787569-0.111013365935-0.1281240893990.28826052802-0.1122921909270.4216404825690.01771447003130.04914490902310.731424075638-0.02130622068150.45501541336854.40228032216.30348621704-25.8032873845
25.50625673739-1.04015705772-3.982238605580.760286864602-0.06706640379782.554875597320.3485703596290.4949312133540.734815484325-0.1668640311680.0520596459124-0.160160410387-0.557490175195-0.109155929625-0.3707641641520.66153366092-0.008367087737470.107315238980.705553255079-0.03483089451830.64031134718242.564620191416.2029020515-17.2657137901
30.5219384401720.126025788225-1.876998050450.8602725844220.05782645080555.814857941120.1825395271830.0502383470310.101867819638-0.0105422167578-0.03466129222430.0393411288134-0.310905440789-0.210942908493-0.1296167670710.321138209305-0.00369339194418-0.002785725136910.586837018714-0.07494069851890.40548804142523.940419906810.54091731697.50052793814
43.65601358336-0.513697142752-0.2949530269553.596701096410.1330125367895.769001582410.165766546589-0.1423527686540.1191029088090.715781944431-0.1091836099910.408655331681-0.166140536768-0.534526441794-0.008827104138940.483188581954-0.1150504160860.09480585410210.480569880914-0.08084137186630.45704366108414.935104920214.53989717739.1645978366
54.03855838352-1.817834765992.102512231086.59628860106-2.122472980146.164182299110.0830860301505-0.0385848218495-0.50107409493-0.3670942947320.0785526633562-0.4680327774661.100277454780.293389540812-0.1911546740010.7240268568040.05567095910350.04825075376620.3520415323210.04096114427190.75642585958248.8143809219-25.259913090392.9368793981
65.48015680473-2.040107731383.324563322138.4426083327-1.186083003616.050922127260.246566821391-0.56291474512-0.8254472827120.0616691722860.4513137838640.4319984613380.809761590242-1.15041099321-0.367742258610.50642062473-0.06948594944320.0369797701710.4887632226530.09084052706930.60659735649338.6120455931-17.734467714791.7901040104
73.14174112741-1.680333890190.05907065493435.07774552661-1.737974739553.594241246640.133928513728-0.285753822384-0.2714596631920.5032159896240.1192737746490.1259955901320.0743526985222-0.487085725093-0.1335933333630.605689126443-0.02859569046930.1086288929060.4234119796720.04189001265770.56605507763140.2768647675-4.1747140841786.8047359717
80.485424682794-0.3069023773890.7115049893113.34506311295-3.896318605164.89247951258-0.163166011188-0.117081005332-0.02938108815990.278413614120.1696997347620.210352902364-0.223388859083-0.479883159356-0.002825074909210.3924076787630.05979322810490.03278628657370.310869899031-0.003588843610990.3814311571440.090384167611.504331803671.6911115445
96.385649082340.4390604497251.987304459232.50654075031-1.243265264925.39559218732-0.2929221067040.9043447156351.09806074112-0.566838927070.1040235011440.223293328327-0.5327355919730.1113407854490.07267753672720.613289798064-0.0630592667256-0.04086280770260.4354483790770.1075403008380.57047156278435.179400491526.746556977945.3325263854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 243 )
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 328 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 51 )
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 93 )
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 224 )
9X-RAY DIFFRACTION9chain 'B' and (resid 225 through 327 )

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