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- PDB-6fu4: Ligand binding domain (LBD) of the p. aeruginosa histamine recept... -

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Basic information

Entry
Database: PDB / ID: 6fu4
TitleLigand binding domain (LBD) of the p. aeruginosa histamine receptor TlpQ
ComponentsProbable chemotaxis transducer
KeywordsSIGNALING PROTEIN / chemotaxis / Pseudomonas aeruginosa / chemoreceptor / histamine
Function / homology
Function and homology information


membrane => GO:0016020 / signal transduction
Similarity search - Function
Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
ACETATE ION / HISTAMINE / PHOSPHATE ION / Probable chemotaxis transducer
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.45 Å
AuthorsGavira, J.A. / Krell, T. / Conejero-Muriel, M. / Corral-Lugo, A. / Matilla, M.A. / Silva Jimenez, H. / Mesa Torres, N. / Martin-Mora, D.
Funding support Spain, 2items
OrganizationGrant numberCountry
MICINNBIO2013-4297-P Spain
MICINNBIO2016-74875-P Spain
CitationJournal: MBio / Year: 2018
Title: High-Affinity Chemotaxis to Histamine Mediated by the TlpQ Chemoreceptor of the Human Pathogen Pseudomonas aeruginosa.
Authors: Corral-Lugo, A. / Matilla, M.A. / Martin-Mora, D. / Silva Jimenez, H. / Mesa Torres, N. / Kato, J. / Hida, A. / Oku, S. / Conejero-Muriel, M. / Gavira, J.A. / Krell, T.
History
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable chemotaxis transducer
B: Probable chemotaxis transducer
C: Probable chemotaxis transducer
D: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,65015
Polymers152,5884
Non-polymers1,06211
Water5,495305
1
A: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4454
Polymers38,1471
Non-polymers2983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3503
Polymers38,1471
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5045
Polymers38,1471
Non-polymers3574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3503
Polymers38,1471
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.616, 103.983, 147.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Probable chemotaxis transducer / LBD TlpQ


Mass: 38146.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA2654 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I0I4

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Non-polymers , 5 types, 316 molecules

#2: Chemical
ChemComp-HSM / HISTAMINE / Histamine


Mass: 111.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9N3 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, hormone*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 5.6
Details: Counterdiffusion 1.5 M ammonium phosphate, 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97917, 0.97901, 0.97670
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.979011
30.97671
ReflectionResolution: 2.45→84.98 Å / Num. obs: 46027 / % possible obs: 98.12 % / Redundancy: 3.9 % / Biso Wilson estimate: 41.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4544 / CC1/2: 0.826 / % possible all: 98.06

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.45→84.98 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.237 -5 %Random
Rwork0.193 ---
obs-46027 98.12 %-
Displacement parametersBiso mean: 52.22 Å2
Refinement stepCycle: LAST / Resolution: 2.45→84.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9065 0 70 305 9440

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