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- PDB-4xmq: Crystal structure of the sensory domain of the Campylobacter jeju... -

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Basic information

Entry
Database: PDB / ID: 4xmq
TitleCrystal structure of the sensory domain of the Campylobacter jejuni chemoreceptor Tlp3 (CcmL)
ComponentsPutative methyl-accepting chemotaxis signal transduction protein
KeywordsSIGNALING PROTEIN / Sensory domain / chemotactic receptor
Function / homology
Function and homology information


signal transduction / membrane
Similarity search - Function
Methyl-accepting chemotaxis protein-like, first PDC sensor domain / 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). / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Methyl-accepting chemotaxis signal transduction protein
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRoujeinikova, A. / Liu, Y.C. / Machuca, M.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains.
Authors: Liu, Y.C. / Machuca, M.A. / Beckham, S.A. / Gunzburg, M.J. / Roujeinikova, A.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Sep 27, 2023Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyl-accepting chemotaxis signal transduction protein
B: Putative methyl-accepting chemotaxis signal transduction protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4973
Polymers57,4012
Non-polymers961
Water15,349852
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-21 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.330, 137.510, 49.100
Angle α, β, γ (deg.)90.000, 94.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative methyl-accepting chemotaxis signal transduction protein


Mass: 28700.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) (Campylobacter)
Strain: NCTC 11168 / Gene: Cj1564 / Plasmid: pET151/D-Topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q0P864
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Ammonium Sulfate / PH range: Sodium Citrate pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→29.95 Å / Num. obs: 75588 / % possible obs: 84.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3491 / % possible all: 79.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xmr

4xmr


Resolution: 1.5→26.9 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.357 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 3777 5 %RANDOM
Rwork0.1382 71768 --
obs0.1407 -84.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.22 Å2 / Biso mean: 25.849 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.02 Å2
2---0.87 Å20 Å2
3---0.93 Å2
Refinement stepCycle: final / Resolution: 1.5→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 5 852 4846
Biso mean--33.15 35.92 -
Num. residues----501
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 244 -
Rwork0.21 4958 -
all-5202 -
obs--79.25 %

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