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

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Basic information

Entry
Database: PDB / ID: 5ltx
TitleLIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID CHEMORECEPTOR PCTA IN COMPLEX WITH L-MET
ComponentsChemotaxis proteinChemotaxis
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 / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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). ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Chemotaxis methyl-accepting receptor / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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 / FORMIC ACID / METHIONINE / Methyl-accepting chemotaxis protein PctA / Methyl-accepting chemotaxis protein PctA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGavira, J.A. / Rico-Gimenez, M. / Ortega, A. / Conejero-Muriel, M. / Zhulin, I. / Krell, T.
Funding support Spain, 1items
OrganizationGrant numberCountry
MICINNBIO2013-4297-P Spain
CitationJournal: Mbio / Year: 2020
Title: How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Authors: Gavira, J.A. / Jimenez-Rico, M. / Pineda-Molina, E. / Krell, T.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
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 / _struct.title
Revision 1.2Jan 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: Chemotaxis protein
B: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,82314
Polymers58,9472
Non-polymers87712
Water6,738374
1
A: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9257
Polymers29,4731
Non-polymers4516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8997
Polymers29,4731
Non-polymers4256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.680, 76.555, 116.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chemotaxis protein / Chemotaxis / Methyl-accepting chemotaxis protein PctA / PctA-LBD


Mass: 29473.318 Da / Num. of mol.: 2 / Fragment: ligand binding domain, UNP residues 30-278
Source method: isolated from a genetically manipulated source
Details: PctA Ligand binding domain / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pctA_1, mcpB_2, AO946_32780, AOY09_01348, PAERUG_P32_London_17_VIM_2_10_11_00198
Plasmid: PET28B PLUS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H0Z019, UniProt: G3XD24*PLUS

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Non-polymers , 5 types, 386 molecules

#2: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6
Details: Capillary counter diffusion: 2.0 M sodium formate & 0.1 M Na Act pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.02→47.73 Å / Num. obs: 42626 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.02-2.094.80.9970.68199.1
7.82-47.734.60.0230.999199.1

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Processing

Software
NameVersionClassification
Aimless0.3.3data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T65

5t65


Resolution: 2.02→46.358 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 2145 5.04 %Random
Rwork0.1877 ---
obs0.1892 42572 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.34 Å2 / Biso mean: 43.3498 Å2 / Biso min: 17.34 Å2
Refinement stepCycle: final / Resolution: 2.02→46.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 56 374 4086
Biso mean--54.03 47.86 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044198
X-RAY DIFFRACTIONf_angle_d0.6845740
X-RAY DIFFRACTIONf_chiral_restr0.046643
X-RAY DIFFRACTIONf_plane_restr0.006761
X-RAY DIFFRACTIONf_dihedral_angle_d13.9222564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.0670.27051290.2672623275299
2.067-2.11870.2691440.26722649279399
2.1187-2.1760.29991490.237326532802100
2.176-2.240.24791400.238926682808100
2.24-2.31230.2991520.229226472799100
2.3123-2.3950.26761450.218426782823100
2.395-2.49090.24421340.219126832817100
2.4909-2.60420.25611270.211826832810100
2.6042-2.74150.20811300.202327232853100
2.7415-2.91320.22361480.196226882836100
2.9132-3.13810.2391720.19512653282599
3.1381-3.45380.2211450.16527062851100
3.4538-3.95340.16261540.161127162870100
3.9534-4.97990.19061240.14922785290999
4.9799-46.36970.2061520.18482872302499
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)
15.73251.16145.8388-0.511.35334.86620.02610.29620.32340.1105-0.0347-0.01740.11020.259-0.0060.3682-0.02850.00180.33930.02840.3502-11.26414.125-5.9816
22.62331.4013-0.17292.07560.08922.77850.2183-0.09690.14570.1759-0.13780.1946-0.0179-0.1823-0.05640.2059-0.01020.03720.1559-0.00630.1894-35.14823.3332-15.1342
35.62080.06272.43053.53120.08863.70990.1219-0.0883-0.2240.1761-0.0351-0.28230.2140.0044-0.08330.2406-0.0614-0.00990.20890.00710.2062-11.88434.95113.0206
44.531-0.55742.64791.89540.33633.531-0.1483-0.337-0.23670.44130.2059-0.58370.25590.5329-0.02980.45060.12170.02590.41980.06060.4239-9.524312.1495-20.3706
52.3076-0.6445-0.38313.8769-0.60582.07430.06470.04830.1260.5996-0.0213-0.0402-0.05060.0247-0.03360.27850.01080.00050.19270.01170.2114-23.99223.3494-36.1069
66.36390.40731.94221.67210.3192.5443-0.4475-0.14770.75730.2260.1584-0.3685-0.30620.57420.2560.3240.0569-0.07390.378-0.01340.3932-7.15622.2104-28.2584
75.51410.4162-0.23782.37090.39945.8735-0.18330.18550.29470.18780.0388-1.05450.19411.62760.26010.3710.1068-0.13550.9533-0.02980.7210.916718.9341-25.5038
82.0789-0.05911.2371.8739-0.52594.0815-0.10610.205-0.00960.48790.2444-0.6772-0.11120.684-0.070.33270.1463-0.09630.4943-0.10290.50263.015417.1577-19.7423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 77 )A30 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 183 )A78 - 183
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 272 )A184 - 272
4X-RAY DIFFRACTION4chain 'B' and (resid 37 through 77 )B37 - 77
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 153 )B78 - 153
6X-RAY DIFFRACTION6chain 'B' and (resid 154 through 219 )B154 - 219
7X-RAY DIFFRACTION7chain 'B' and (resid 220 through 247 )B220 - 247
8X-RAY DIFFRACTION8chain 'B' and (resid 248 through 271 )B248 - 271

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