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- PDB-6d8v: Methyl-accepting Chemotaxis protein X -

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Basic information

Entry
Database: PDB / ID: 6d8v
TitleMethyl-accepting Chemotaxis protein X
ComponentsProbable chemoreceptor (Methyl-accepting chemotaxis) transmembrane protein
KeywordsMEMBRANE PROTEIN / MCP / Chemotaxis
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / membrane => GO:0016020 / signal transduction
Similarity search - Function
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). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
1,1-DIMETHYL-PROLINIUM / Probable chemoreceptor (Methyl-accepting chemotaxis) transmembrane protein
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShrestha, M. / Schubot, F.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1253234 United States
CitationJournal: Biochem. J. / Year: 2018
Title: Structure of the sensory domain of McpX fromSinorhizobium meliloti, the first known bacterial chemotactic sensor for quaternary ammonium compounds.
Authors: Shrestha, M. / Compton, K.K. / Mancl, J.M. / Webb, B.A. / Brown, A.M. / Scharf, B.E. / Schubot, F.D.
History
DepositionApr 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Probable chemoreceptor (Methyl-accepting chemotaxis) transmembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9843
Polymers28,7181
Non-polymers2662
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.040, 119.040, 121.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Probable chemoreceptor (Methyl-accepting chemotaxis) transmembrane protein


Mass: 28718.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: mcpX, SMc01104 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92SH9
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PBE / 1,1-DIMETHYL-PROLINIUM / PROLINE BETAINE


Mass: 144.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.08 Å3/Da / Density % sol: 69.85 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.08M Sodium acetate 1.6M Ammonium sulfate 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→78.66 Å / Num. obs: 13433 / % possible obs: 99.7 % / Redundancy: 7 % / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→78.63 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 638 5.01 %
Rwork0.2065 12088 -
obs0.2086 12726 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.79 Å2 / Biso mean: 95.5076 Å2 / Biso min: 42.37 Å2
Refinement stepCycle: final / Resolution: 2.8→78.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 30 2 2044
Biso mean--115.93 72.6 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052073
X-RAY DIFFRACTIONf_angle_d0.7342814
X-RAY DIFFRACTIONf_chiral_restr0.045306
X-RAY DIFFRACTIONf_plane_restr0.005369
X-RAY DIFFRACTIONf_dihedral_angle_d16.3091217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-3.01630.36551260.35272382250899
3.0163-3.31980.28751250.25132390251598
3.3198-3.80020.27071270.2242399252698
3.8002-4.78780.20971270.16492423255098
4.7878-78.66070.22811330.19612494262794
Refinement TLS params.Method: refined / Origin x: 43.8551 Å / Origin y: 55.7719 Å / Origin z: 126.2002 Å
111213212223313233
T0.2578 Å2-0.0153 Å2-0.0202 Å2-0.9854 Å2-0.0425 Å2--0.5535 Å2
L5.4596 °20.0197 °20.9705 °2-2.2136 °2-0.3566 °2--3.361 °2
S0.2491 Å °-0.8634 Å °0.3536 Å °0.1614 Å °-0.246 Å °-0.2243 Å °-0.1374 Å °0.3815 Å °0.0039 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA38 - 306
2X-RAY DIFFRACTION1allC2
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allS1 - 2

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