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- PDB-9kpj: Crystal structure of Helicobacter pylori chemoreceptor TlpA ligan... -

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Basic information

Entry
Database: PDB / ID: 9kpj
TitleCrystal structure of Helicobacter pylori chemoreceptor TlpA ligand-binding domain in complex with indole
ComponentsMethyl-accepting chemotaxis protein TlpA
KeywordsSIGNALING PROTEIN / Chemoreceptor / Indole / Helicobacter pylori / Ligand-binding domain
Function / homologyINDOLE / :
Function and homology information
Biological speciesHelicobacter pylori PMSS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsWang, X. / Bi, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370116 China
CitationJournal: Curr.Biol. / Year: 2025
Title: Discovery of an indole-sensing chemoreceptor in Helicobacter pylori.
Authors: Wang, X. / Xu, W. / Yao, F. / Liu, S. / Zhang, Y. / Sourjik, V. / Bi, S.
History
DepositionNov 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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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)33,5217
Polymers33,0931
Non-polymers4276
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.586, 168.571, 132.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

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Components

#1: Protein Methyl-accepting chemotaxis protein TlpA


Mass: 33093.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori PMSS1 (bacteria) / Gene: tlpA, HPYLPMSS1_00094 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAN1AVD9
#2: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.04 M Citric acid, 0.06 M BIS-TRIS propane, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2024
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.01→42.143 Å / Num. obs: 21323 / % possible obs: 93.04 % / Redundancy: 12.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1537 / Rpim(I) all: 0.04498 / Rrim(I) all: 0.1604 / Net I/σ(I): 12.92
Reflection shellResolution: 2.01→2.082 Å / Rmerge(I) obs: 1.759 / Num. unique obs: 1459 / CC1/2: 0.746 / CC star: 0.925 / Rpim(I) all: 0.5131 / Rrim(I) all: 1.835 / % possible all: 64.7

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Processing

Software
NameVersionClassification
PHENIX1.15refinement
XDSdata reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→42.143 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1034 4.88 %
Rwork0.1754 --
obs0.1777 21200 93.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→42.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 29 149 2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072183
X-RAY DIFFRACTIONf_angle_d0.8652926
X-RAY DIFFRACTIONf_dihedral_angle_d18.2311356
X-RAY DIFFRACTIONf_chiral_restr0.051338
X-RAY DIFFRACTIONf_plane_restr0.005368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.1160.25531300.21312065X-RAY DIFFRACTION68
2.116-2.24860.26091560.20112874X-RAY DIFFRACTION96
2.2486-2.42220.25541130.18523027X-RAY DIFFRACTION98
2.4222-2.66590.21871610.17822991X-RAY DIFFRACTION97
2.6659-3.05150.2121660.1832994X-RAY DIFFRACTION98
3.0515-3.84420.24641460.17383036X-RAY DIFFRACTION97
3.8442-42.1430.21620.15883179X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4659-0.31220.18434.4523-1.46382.2087-0.0194-0.0276-0.01010.15910.046-0.106-0.19590.1417-0.02420.0737-0.0346-0.00040.18550.00230.1529-3.537-37.372622.447
20.40890.46270.22911.168-0.08780.4671-0.06080.15190.1302-0.0647-0.1267-0.0543-0.4916-0.04160.05740.60280.02060.09180.13840.11520.228-6.779-12.49191.9324
31.5137-0.03-0.60110.77820.37961.59830.1426-0.0891-0.10620.3016-0.08830.6956-0.3516-0.0888-0.1360.63560.04790.14180.27580.02820.4372-16.509-15.21553.3359
41.32730.8103-0.03851.9951-0.52060.16530.1714-0.06220.25570.320.03110.2259-0.4487-0.3122-0.01120.38290.05820.09610.23060.01720.235-15.5461-23.13897.0174
51.03920.414-0.18631.98-0.64721.8024-0.0004-0.01180.0396-0.23890.01610.1553-0.1745-0.0920.01630.10290.0183-0.00160.19170.02020.1358-14.827-34.626314.0597
60.77870.50340.80333.53081.21452.90270.17320.007-0.16740.05010.1113-0.15410.02890.139-0.14030.1307-0.0213-0.02180.23110.0140.2237-15.4278-51.099120.5569
72.1422-0.09990.69214.6978-0.83922.80960.0168-0.0697-0.04830.14650.1259-0.0892-0.0970.0107-0.11080.051-0.0105-0.00240.2024-0.00280.1472-10.6534-41.752521.6305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 144 )
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 217 )
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 232 )
7X-RAY DIFFRACTION7chain 'A' and (resid 233 through 270 )

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