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- PDB-6dtm: Crystal Structure of Helicobacter pylori TlpA Chemoreceptor Ligan... -

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Basic information

Entry
Database: PDB / ID: 6dtm
TitleCrystal Structure of Helicobacter pylori TlpA Chemoreceptor Ligand Binding Domain
ComponentsMethyl-accepting chemotaxis protein TlpA
KeywordsSIGNALING PROTEIN / chemoreceptor / helix bundle / PAS/Cache
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). / signal transduction / metal ion binding / membrane / Methyl-accepting chemotaxis protein TlpA
Function and homology information
Biological speciesHelicobacter pylori SS1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRemington, S.J. / Guillemin, K. / Sweeney, E. / Perkins, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Protein Sci. / Year: 2018
Title: Structures of the ligand-binding domain of Helicobacter pylori chemoreceptor TlpA.
Authors: Sweeney, E.G. / Perkins, A. / Kallio, K. / James Remington, S. / Guillemin, K.
History
DepositionJun 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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: Methyl-accepting chemotaxis protein TlpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5882
Polymers33,5531
Non-polymers351
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Presumed nonphysiological state
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area13170 Å2
Unit cell
Length a, b, c (Å)143.220, 67.830, 29.415
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-481-

HOH

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Components

#1: Protein Methyl-accepting chemotaxis protein TlpA


Mass: 33552.719 Da / Num. of mol.: 1 / Fragment: periplasmic ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori SS1 (bacteria) / Gene: tlpA, HPYLSS1_00094 / Plasmid: pBH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1U9IS38
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: depends on crystal / PH range: 6, 6.5 or 7 depending on crystal

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Feb 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→29.3 Å / Num. obs: 16013 / % possible obs: 97.3 % / Redundancy: 7.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.049 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.788 / Rpim(I) all: 0.397 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
SAINTdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.342 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.323 497 5.11 %
Rwork0.2221 --
obs0.2275 9724 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 1 84 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181959
X-RAY DIFFRACTIONf_angle_d1.6472644
X-RAY DIFFRACTIONf_dihedral_angle_d17.7971212
X-RAY DIFFRACTIONf_chiral_restr0.072320
X-RAY DIFFRACTIONf_plane_restr0.009330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.75170.39161280.26032254X-RAY DIFFRACTION97
2.7517-3.14950.40461150.25382282X-RAY DIFFRACTION99
3.1495-3.96650.33141300.21952327X-RAY DIFFRACTION100
3.9665-29.34360.25181240.19512364X-RAY DIFFRACTION100

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