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- PDB-6e09: Crystal Structure of Helicobacter pylori TlpA Chemoreceptor Ligan... -

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Basic information

Entry
Database: PDB / ID: 6000000000
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 / membrane / metal ion binding / Methyl-accepting chemotaxis protein TlpA
Function and homology information
Biological speciesHelicobacter pylori SS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 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)R01 DK101314 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
DepositionJul 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein TlpA
B: Methyl-accepting chemotaxis protein TlpA
C: Methyl-accepting chemotaxis protein TlpA
D: Methyl-accepting chemotaxis protein TlpA


Theoretical massNumber of molelcules
Total (without water)136,2744
Polymers136,2744
Non-polymers00
Water9,530529
1
A: Methyl-accepting chemotaxis protein TlpA
D: Methyl-accepting chemotaxis protein TlpA


Theoretical massNumber of molelcules
Total (without water)68,1372
Polymers68,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-20 kcal/mol
Surface area25010 Å2
MethodPISA
2
B: Methyl-accepting chemotaxis protein TlpA
C: Methyl-accepting chemotaxis protein TlpA


Theoretical massNumber of molelcules
Total (without water)68,1372
Polymers68,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-18 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.501, 72.354, 132.921
Angle α, β, γ (deg.)90.00, 93.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methyl-accepting chemotaxis protein TlpA


Mass: 34068.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori SS1 (bacteria) / Gene: tlpA, HPYLSS1_00094 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: A0A1U9IS38
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% PEG 3350, 0.15M AmNO3, 0.15M NaCl, 25mM HEPES pH 7.5, 2mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 34-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→27 Å / Num. obs: 97102 / % possible obs: 99.9 % / Redundancy: 23 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.059 / Net I/av σ(I): 13.2 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 4.3 / CC1/2: 0.948 / Rpim(I) all: 0.703 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→26.703 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2464 3733 3.84 %
Rwork0.1897 --
obs0.192 97102 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→26.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7885 0 0 529 8414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148013
X-RAY DIFFRACTIONf_angle_d1.310790
X-RAY DIFFRACTIONf_dihedral_angle_d12.5554965
X-RAY DIFFRACTIONf_chiral_restr0.0631293
X-RAY DIFFRACTIONf_plane_restr0.0081346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32910.3094920.212657X-RAY DIFFRACTION70
2.3291-2.35970.31791260.22172747X-RAY DIFFRACTION74
2.3597-2.3920.26861130.22492817X-RAY DIFFRACTION76
2.392-2.42620.24961130.22782985X-RAY DIFFRACTION79
2.4262-2.46240.29331040.21573077X-RAY DIFFRACTION83
2.4624-2.50080.26871570.21653114X-RAY DIFFRACTION85
2.5008-2.54180.29931310.21293391X-RAY DIFFRACTION89
2.5418-2.58560.26611290.20733376X-RAY DIFFRACTION90
2.5856-2.63260.25431480.2133381X-RAY DIFFRACTION92
2.6326-2.68310.29981300.21313574X-RAY DIFFRACTION94
2.6831-2.73790.24131550.21713585X-RAY DIFFRACTION96
2.7379-2.79730.28571190.20983599X-RAY DIFFRACTION97
2.7973-2.86230.27351490.20083685X-RAY DIFFRACTION98
2.8623-2.93380.31351450.20993712X-RAY DIFFRACTION99
2.9338-3.0130.291510.19733717X-RAY DIFFRACTION99
3.013-3.10160.26451530.19313692X-RAY DIFFRACTION100
3.1016-3.20150.24031410.19553729X-RAY DIFFRACTION100
3.2015-3.31580.25341400.19423745X-RAY DIFFRACTION100
3.3158-3.44830.24451590.18223697X-RAY DIFFRACTION100
3.4483-3.60480.23821420.18143591X-RAY DIFFRACTION96
3.6048-3.79440.22771340.17733528X-RAY DIFFRACTION94
3.7944-4.03140.21461560.15693736X-RAY DIFFRACTION100
4.0314-4.34140.18731560.15463691X-RAY DIFFRACTION100
4.3414-4.77610.18161530.13893728X-RAY DIFFRACTION100
4.7761-5.4620.20681450.16883704X-RAY DIFFRACTION100
5.462-6.86220.27181580.22313761X-RAY DIFFRACTION100
6.8622-26.70520.29821340.2193350X-RAY DIFFRACTION90

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