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- PDB-5wbf: Double CACHE (dCACHE) sensing domain of TlpC chemoreceptor from H... -

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Basic information

Entry
Database: PDB / ID: 5wbf
TitleDouble CACHE (dCACHE) sensing domain of TlpC chemoreceptor from Helicobacter pylori
ComponentsMethyl-accepting chemotaxis transducer (TlpC)
KeywordsSIGNALING PROTEIN / Bacterial protein / Chemoreceptor sensing domain / double-CACHE domain / Helicobacter pylori
Function / homologyMethyl-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). / membrane => GO:0016020 / signal transduction / LACTIC ACID / Methyl-accepting chemotaxis transducer (TlpC)
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.19 Å
AuthorsMachuca, M.A. / Johnson, K.S. / Liu, Y.C. / Steer, D.L. / Ottemann, K.M. / Roujeinikova, A.
CitationJournal: Sci Rep / Year: 2017
Title: Helicobacter pylori chemoreceptor TlpC mediates chemotaxis to lactate.
Authors: Machuca, M.A. / Johnson, K.S. / Liu, Y.C. / Steer, D.L. / Ottemann, K.M. / Roujeinikova, A.
History
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 transducer (TlpC)
B: Methyl-accepting chemotaxis transducer (TlpC)
C: Methyl-accepting chemotaxis transducer (TlpC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1717
Polymers91,8083
Non-polymers3624
Water8,143452
1
A: Methyl-accepting chemotaxis transducer (TlpC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6932
Polymers30,6031
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl-accepting chemotaxis transducer (TlpC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6932
Polymers30,6031
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methyl-accepting chemotaxis transducer (TlpC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7853
Polymers30,6031
Non-polymers1822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)189.33, 103.17, 61.79
Angle α, β, γ (deg.)90, 98.32, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-accepting chemotaxis transducer (TlpC)


Mass: 30602.799 Da / Num. of mol.: 3
Fragment: Double CACHE (dCACHE) sensing domain (UNP residues 34-297)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_0082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O24911
#2: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 452 / 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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl2, 0.1 M MES/NaOH (pH 6.5), 22% (w/v) PEG 4000 and 10 mM BaCl2H4O2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.5498 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.19→30.57 Å / Num. obs: 59028 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.038 / Rrim(I) all: 0.073 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.19-2.313.60.285.33080384720.9040.170.3295.396.3
6.93-30.573.50.037609217630.9960.0230.04422.389.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless3.3.21data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
PHENIX1.9_1692model building
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.19→30.57 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2179 2951 -
Rwork0.1818 --
obs-59028 97.6 %
Refinement stepCycle: LAST / Resolution: 2.19→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 0 24 452 6675
LS refinement shellResolution: 2.19→2.31 Å

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