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- PDB-6sy9: Structure of the Legionella pneumophila response regulator LqsR -

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Basic information

Entry
Database: PDB / ID: 6sy9
TitleStructure of the Legionella pneumophila response regulator LqsR
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / response regulator / receiver domain / output domain
Function / homologyphosphorelay signal transduction system / Response regulator receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / (Two component) response regulator
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHochstrasser, R. / Hutter, C.A.J. / Arnold, F.M. / Baerlocher, K. / Seeger, M.A. / Hilbi, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_153200, 31003A_175557, PP00P3_144823 Switzerland
CitationJournal: Mol.Microbiol. / Year: 2020
Title: The structure of the Legionella response regulator LqsR reveals amino acids critical for phosphorylation and dimerization.
Authors: Hochstrasser, R. / Hutter, C.A.J. / Arnold, F.M. / Barlocher, K. / Seeger, M.A. / Hilbi, H.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 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: Response regulator


Theoretical massNumber of molelcules
Total (without water)41,4941
Polymers41,4941
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15710 Å2
Unit cell
Length a, b, c (Å)50.100, 67.840, 116.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Response regulator / Response regulator FixJ / Response regulator containing a CheY-like receiver domain and an HD-GYP domain


Mass: 41493.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria)
Gene: C3926_14995, C3927_13800, D7214_05345, ERS240541_01816, ERS253249_00465, NCTC12000_02932
Plasmid: pET28(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A130R805, UniProt: Q5ZRY9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Sodium formate, 0.1M Bis-Tris propane, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.031 Å / Num. obs: 23899 / % possible obs: 100 % / Redundancy: 13.041 % / Biso Wilson estimate: 49.216 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.093 / Χ2: 1.003 / Net I/σ(I): 20.98 / Num. measured all: 311660 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.1513.5771.951.6723515173217320.6392.027100
2.15-2.2113.3111.3972.2222549169416940.7591.453100
2.21-2.2812.7951.1292.7621329166716670.8321.176100
2.28-2.3512.6910.8513.6219899156815680.8850.887100
2.35-2.4213.7370.6574.8321526156715670.9350.682100
2.42-2.5113.6170.496.2720630151515150.9630.509100
2.51-2.613.4260.3947.9219467145014500.9730.41100
2.6-2.7113.0690.3159.5918401140814080.9780.327100
2.71-2.8312.4070.2411.7616712134713470.9880.25100
2.83-2.9713.4770.17915.917331128612860.9940.186100
2.97-3.1313.5790.13121.0116974125012500.9960.136100
3.13-3.3213.4740.09926.2215616115911590.9980.103100
3.32-3.5512.8580.06436.6514221110611060.9990.067100
3.55-3.8312.3650.04745.5912773103310330.9990.05100
3.83-4.213.250.03855.63127339619610.9990.039100
4.2-4.712.8910.03264.641113886486410.033100
4.7-5.4211.7710.03260.82909977377310.034100
5.42-6.6412.3980.03360.282826686680.9990.034100
6.64-9.3911.7020.02572.85623753453310.02699.8
9.39-46.03110.1510.0283.16322832131810.02199.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.1→46.031 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1195 5 %
Rwork0.2021 22698 -
obs0.2035 23893 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.98 Å2 / Biso mean: 56.5765 Å2 / Biso min: 26.89 Å2
Refinement stepCycle: final / Resolution: 2.1→46.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 128 2620
Biso mean---52.86 -
Num. residues----307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.18410.33731300.29672480
2.1841-2.28350.2431310.26042477
2.2835-2.40390.2611300.23552480
2.4039-2.55450.29761310.22222481
2.5545-2.75170.25411310.22222492
2.7517-3.02850.2461320.2242513
3.0285-3.46660.23811330.20142524
3.4666-4.36710.19451350.17092565
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)
11.17950.4073-0.04580.2575-0.01150.6928-0.01040.07590.10740.0474-0.03190.0468-0.094-0.033400.3165-0.0091-0.00890.3547-0.04780.361135.918158.242928.1021
20.7075-0.20210.30580.0739-0.41120.11620.2336-0.31730.7180.2872-0.08280.0528-0.2193-0.12740.03060.535-0.0915-0.02280.4686-0.10980.265641.995561.804935.8249
32.07270.4579-0.10042.0641-0.96820.3913-0.00330.12170.0458-0.2101-0.1885-0.2170.03590.3149-0.00010.33680.01080.01260.3559-0.00340.375545.845458.686822.5449
40.40070.2516-0.58411.6692-0.40571.01320.07060.0481-0.2772-0.0942-0.07210.08620.2507-0.0361-00.3414-0.01340.02170.3516-0.03890.378140.053651.522125.9847
51.38011.4249-0.2891.6745-0.35141.93480.1966-0.0445-0.3080.2138-0.02220.19270.07330.0631-00.35750.0181-0.01020.39690.01760.394633.134638.635846.41
60.1288-0.0784-0.00430.54530.12260.41170.2889-0.1759-0.47490.57620.0927-0.06480.2626-0.2260.03280.6781-0.0573-0.05090.49050.16520.444827.901529.22157.2705
71.89170.13050.11030.89840.02081.34280.1263-0.2260.3780.4966-0.02720.1805-0.28090.01890.00080.4840.03820.11080.3826-0.05720.325731.078256.481145.8134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )A2 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 94 )A32 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 147 )A95 - 147
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 188 )A148 - 188
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 257 )A189 - 257
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 303 )A258 - 303
7X-RAY DIFFRACTION7chain 'A' and (resid 304 through 341 )A304 - 341

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