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- PDB-5t65: LIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID C... -

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Basic information

Entry
Database: PDB / ID: 5t65
TitleLIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID CHEMORECEPTOR PCTA IN COMPLEX WITH L-ILE
ComponentsMethyl-accepting chemotaxis protein PctA
KeywordsSIGNALING PROTEIN / LIGAND BINDING DOMAIN / Pseudomonas aeruginosa / CHEMOTACTIC TRANSDUCER
Function / homology
Function and homology information


amino acid binding / response to amino acid / chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Chemotaxis methyl-accepting receptor / 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). / Target SNARE coiled-coil homology domain / HAMP domain ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Chemotaxis methyl-accepting receptor / 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). / Target SNARE coiled-coil homology domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
ACETATE ION / ISOLEUCINE / Methyl-accepting chemotaxis protein PctA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGavira, J.A. / Rico-Jimenez, M. / Ortega, A. / Conejero-Muriel, M. / Zhulin, I. / Krell, T.
Funding support Spain, 1items
OrganizationGrant numberCountry
MICINNBIO2013-4297-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 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Structure summary / Category: audit_author / struct / Item: _struct.title
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 / _citation_author.name
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein PctA
B: Methyl-accepting chemotaxis protein PctA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4237
Polymers58,9472
Non-polymers4765
Water4,468248
1
A: Methyl-accepting chemotaxis protein PctA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7604
Polymers29,4731
Non-polymers2863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein PctA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6643
Polymers29,4731
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.610, 132.610, 77.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Methyl-accepting chemotaxis protein PctA


Mass: 29473.318 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 30-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pctA, PA4309 / Plasmid: PET28B PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G3XD24
#2: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-ISOLEUCINE (ILE): ILE A1264 BOUNDED TO CHAIN A ILE B 1267 BOUNDED TO CHAIN B

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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: 3.6 Å3/Da / Density % sol: 66.08 %
Crystal growTemperature: 293.5 K / Method: liquid diffusion / pH: 5
Details: Capillary COUNTER-DIFFUSION: 2.8 M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE pH 5.0, T 20 C
PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 25, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.2→33.153 Å / Num. obs: 39288 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 38.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/av σ(I): 20.99 / Net I/σ(I): 20.99
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.32 / CC1/2: 0.866 / % possible all: 100

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Processing

Software
NameClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C8C

3c8c


Resolution: 2.2→33.153 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 1973 5 %Random selection
Rwork0.1663 ---
obs0.1681 39271 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 31 248 3947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014015
X-RAY DIFFRACTIONf_angle_d1.1625491
X-RAY DIFFRACTIONf_dihedral_angle_d13.381500
X-RAY DIFFRACTIONf_chiral_restr0.051626
X-RAY DIFFRACTIONf_plane_restr0.005718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.22361530.19822630X-RAY DIFFRACTION100
2.255-2.3160.28591470.1972656X-RAY DIFFRACTION100
2.316-2.38410.25651290.19142636X-RAY DIFFRACTION100
2.3841-2.46110.22621400.18782664X-RAY DIFFRACTION100
2.4611-2.5490.23361340.18332672X-RAY DIFFRACTION100
2.549-2.6510.24851430.17592645X-RAY DIFFRACTION100
2.651-2.77160.24421350.1872648X-RAY DIFFRACTION100
2.7716-2.91760.2181380.19222658X-RAY DIFFRACTION100
2.9176-3.10030.24641380.20132665X-RAY DIFFRACTION100
3.1003-3.33950.23651330.18262689X-RAY DIFFRACTION100
3.3395-3.67520.19061620.16822645X-RAY DIFFRACTION100
3.6752-4.20610.16631330.14382669X-RAY DIFFRACTION100
4.2061-5.29570.16291640.12872673X-RAY DIFFRACTION100
5.2957-33.15620.1951240.1592748X-RAY DIFFRACTION99
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)
10.6188-0.4667-0.60870.94560.95590.6732-0.26480.0023-0.14570.36460.290.24120.20290.0605-0.0030.28920.07070.00050.2773-0.01140.22740.957324.7182-5.178
20.8174-0.7806-0.12620.96560.8411.40510.0267-0.04480.2378-0.03340.015-0.1396-0.19710.0249-0.00010.30270.02880.02020.2649-0.02620.28341.154255.66837.9716
32.2240.00550.30782.62781.54621.18510.1405-0.0203-0.01910.55750.1411-0.0727-0.0025-0.05920.00050.32710.05950.01490.3-0.00690.221847.514845.49414.4987
40.7557-0.9853-0.0261.7217-0.01291.48440.1166-0.2913-0.33110.85760.0924-0.29870.73560.11080.01660.53040.0765-0.08630.3687-0.04090.310447.931525.24697.6266
50.9285-0.16710.40891.29230.96561.01770.2764-0.0479-0.27130.3629-0.0626-0.42190.75180.33070.01240.6050.1656-0.11870.3486-0.04260.387349.828919.13891.2717
61.45930.481-0.370.36290.49381.6123-0.1698-0.1215-0.45570.1050.0889-0.11570.3053-0.0257-0.00850.30490.03190.0470.32760.03450.38727.5329.4413-2.4309
70.88460.70840.29330.9666-0.3940.893-0.13310.15160.28290.07410.01540.1873-0.24130.0661-00.33770.06140.00530.30480.0440.294225.408754.8203-14.9397
80.895-0.1930.10151.7228-0.41110.08820.09110.1787-0.0206-0.4179-0.04270.1870.0698-0.2865-0.00010.39930.05370.03690.33550.02280.309816.183544.4498-13.8607
92.45911.3659-0.3941.4289-1.23271.6423-0.0180.0003-0.4284-0.4369-0.07270.11050.07030.0127-0.00970.22820.02020.01930.2490.0160.255524.162635.0818-10.0836
100.7236-0.2113-0.18650.56730.06940.1216-0.05180.3502-0.4613-0.75420.15670.88830.4124-0.4993-0.00940.4953-0.0576-0.07330.4411-0.04140.700813.301223.5263-14.0991
111.2632-0.533-0.3281.2009-0.88171.0709-0.09220.1761-0.4954-0.36260.10930.3780.2918-0.1111-0.00060.4108-0.00940.04690.3188-0.03670.549118.355620.2683-8.1283
12-0.0061-0.0017-0.01980.2018-0.28430.3887-0.17470.2253-0.8086-0.3552-0.27760.99840.5642-0.1663-0.08340.61810.0150.23110.2544-0.05690.680225.028612.0475-9.9797
130.16810.00670.09950.02050.040.0904-0.046-0.18430.45730.21410.1505-0.04-0.15860.0720.00030.47550.1398-0.00960.7227-0.09280.387433.434348.2555-3.7035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 22 THROUGH 69 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 70 THROUGH 114 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 115 THROUGH 175 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 176 THROUGH 211 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 212 THROUGH 261 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 27 THROUGH 69 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 70 THROUGH 114 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 115 THROUGH 145 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 146 THROUGH 190 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 191 THROUGH 222 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 223 THROUGH 247 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 248 THROUGH 265 )
13X-RAY DIFFRACTION13CHAIN A AND (RESID 1264), CHAIN B AND (RESID 1264)

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