[English] 日本語
Yorodumi
- PDB-6sy9: Structure of the Legionella pneumophila response regulator LqsR -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more