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- PDB-5lto: Ligand binding domain of Pseudomonas aeruginosa PAO1 amino acid c... -

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Basic information

Entry
Database: PDB / ID: 5lto
TitleLigand binding domain of Pseudomonas aeruginosa PAO1 amino acid chemoreceptors PctB in complex with L-Gln
ComponentsMethyl-accepting chemotaxis protein PctB
KeywordsSIGNALING PROTEIN / Ligand binding domain / CHEMOTACTIC TRANSDUCER
Function / homology
Function and homology information


amino acid binding / response to amino acid / chemotaxis / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / 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
GLUTAMINE / HAMP domain-containing protein / Methyl-accepting chemotaxis protein PctB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.459 Å
AuthorsGavira, J.A. / Rico-Jimenez, M. / Conejero-Muriel, M. / Krell, T.
Funding support Spain, 1items
OrganizationGrant numberCountry
MICINNBIO2013-42297-P Spain
Citation
Journal: Mbio / Year: 2020
Title: How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Authors: Gavira, J.A. / Jimenez-Rico, M. / Pineda-Molina, E. / Krell, T.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Purification, crystallization and preliminary crystallographic analysis of the ligand-binding regions of the PctA and PctB chemoreceptors from Pseudomonas aeruginosa in complex with amino acids.
Authors: Rico-Jimenez, M. / Munoz-Martinez, F. / Krell, T. / Gavira, J.A. / Pineda-Molina, E.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
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 1.3Apr 29, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Methyl-accepting chemotaxis protein PctB
B: Methyl-accepting chemotaxis protein PctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3188
Polymers63,6452
Non-polymers6736
Water1629
1
A: Methyl-accepting chemotaxis protein PctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1614
Polymers31,8231
Non-polymers3383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein PctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1574
Polymers31,8231
Non-polymers3343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.427, 111.427, 117.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Methyl-accepting chemotaxis protein PctB


Mass: 31822.553 Da / Num. of mol.: 2 / Fragment: ligand binding domain, UNP residues 30-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pctB_2, AOY09_01347 / Plasmid: PET28B PLUS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6UK01, UniProt: Q9HW91*PLUS
#2: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.5
Details: Capillary counter diffusion: 1.7M NH4 Sulphate, 3.5% PEG 400, 0.1M Na-Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.459→74.628 Å / Num. obs: 11417 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 79.59 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.181 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.459-3.4719.81.0940.6771100
16.003-74.62870.0350.994198.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L79

5l79


Resolution: 3.459→74.628 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 545 4.78 %Random
Rwork0.2169 ---
obs0.2197 11395 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.31 Å2 / Biso mean: 77.1149 Å2 / Biso min: 4.31 Å2
Refinement stepCycle: final / Resolution: 3.459→74.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 41 9 3731
Biso mean--77.18 20.31 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023829
X-RAY DIFFRACTIONf_angle_d0.5345213
X-RAY DIFFRACTIONf_chiral_restr0.039587
X-RAY DIFFRACTIONf_plane_restr0.004676
X-RAY DIFFRACTIONf_dihedral_angle_d13.9922272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.459-3.80710.31831340.23926582792
3.8071-4.35790.28471430.216526692812
4.3579-5.49030.28971280.194327082836
5.4903-74.64520.24351400.226428152955
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)
16.7544-0.7562-3.35771.83710.25763.3903-0.26991.2182-0.3093-0.2123-0.26660.12380.1916-1.09610.46960.40290.0048-0.11590.659-0.05330.497146.039656.1211.4816
28.16930.9039-0.51499.7239-0.08047.4705-0.2416-1.3157-0.28420.5789-0.00130.4358-0.4832-0.32650.33560.55790.0036-0.06120.57570.0380.391236.527959.813127.1324
32.640.8154-0.05785.02090.89086.3249-0.2046-0.06270.08030.38690.14920.0185-0.9323-0.17080.11690.56180.0734-0.10880.4817-0.04860.43141.714470.871720.8607
45.2848-0.4881-3.34123.99691.07535.7235-0.3533-0.0844-0.0999-0.23280.1571-0.38850.23840.82940.23610.3796-0.031-0.14810.52490.07090.481651.954959.44069.0242
51.51412.3207-2.48113.7074-3.90624.13380.0157-0.320.9881.2125-0.5739-0.5182-1.49911.37020.32440.6176-0.2161-0.03870.9081-0.18610.900458.358569.68195.056
67.1748-1.699-3.50012.5522-2.90058.15990.40480.02070.077-0.5382-0.0602-0.6693-0.64560.4639-0.30160.7232-0.122-0.04230.7678-0.03950.822161.794666.6507-6.4651
75.2557-1.2445-1.55064.6706-0.20716.06750.46320.51820.5382-0.4635-0.1316-0.56790.0290.4804-0.27610.38510.0221-0.05270.57090.0220.505156.230258.6331-4.5453
86.87871.739326.29932.00012-0.05520.071-0.11130.26650.01880.12370.4575-0.09090.10030.6587-0.0391-0.07370.2712-0.14691.13546.21968.930724.3154
92.4803-1.6157-2.40554.95296.0478.3104-0.0036-0.5407-0.6155-0.09971.2096-1.15610.08072.1598-1.22440.44330.0436-0.04610.8207-0.08590.753136.164736.059312.9009
106.4296-0.4911-2.71899.1588-5.32985.99040.0461-0.40430.39491.3611-0.07750.3463-1.7098-0.52720.43890.57760.0190.01760.728-0.02530.614626.221654.403527.6623
113.7262-1.1835-1.86715.1371.73235.15080.0222-0.1086-0.50960.06260.10760.0620.15180.1684-0.27920.3716-0.0136-0.06750.6659-0.0010.563823.664337.836623.1107
121.93580.1418-2.75496.95661.60034.3532-0.42990.0132-0.7220.91510.7009-0.8531.2629-0.1446-0.19570.85140.0638-0.18060.7549-0.20030.931628.498619.631610.7319
134.2442-4.0266-5.12436.11934.00766.8750.99930.49590.5274-1.1032-1.03340.1145-1.2335-0.739-0.08990.951-0.081-0.15680.7179-0.05240.767643.044112.6751-19.1025
142.9538-8.98722.11642-7.85481.9724-0.4194-0.20770.24571.27850.2418-0.5031-0.5897-0.52430.23540.59610.2232-0.11881.11660.16740.362517.657640.943225.3995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 77 )A36 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 99 )A78 - 99
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 165 )A100 - 165
4X-RAY DIFFRACTION4chain 'A' and (resid 166 through 197 )A166 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 219 )A198 - 219
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 247 )A220 - 247
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 272 )A248 - 272
8X-RAY DIFFRACTION8chain 'A' and (resid 300 through 300 )A300
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 76 )B42 - 76
10X-RAY DIFFRACTION10chain 'B' and (resid 77 through 96 )B77 - 96
11X-RAY DIFFRACTION11chain 'B' and (resid 97 through 198 )B97 - 198
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 263 )B199 - 263
13X-RAY DIFFRACTION13chain 'B' and (resid 264 through 293 )B264 - 293
14X-RAY DIFFRACTION14chain 'B' and (resid 300 through 300 )B300

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