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- PDB-9hvj: Ligand binding domain of Roseburia intestinalis L1-82 uracil chem... -

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Basic information

Entry
Database: PDB / ID: 9hvj
TitleLigand binding domain of Roseburia intestinalis L1-82 uracil chemoreceptor (dCache) in complex with uracil and acetate
ComponentsCache domain protein
KeywordsSIGNALING PROTEIN / Chemoreceptor / dCache domain / Uracil / Acetate / Chemotaxis
Function / homology
Function and homology information


chemotaxis / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / 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 profile. / HAMP domain
Similarity search - Domain/homology
ACETATE ION / URACIL / Cache domain protein
Similarity search - Component
Biological speciesRoseburia intestinalis L1-82 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsJalomo-Khayrova, E. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)464366151 Germany
CitationJournal: Biorxiv / Year: 2025
Title: Specificities of Chemosensory Receptors in the Human Gut Microbiota.
Authors: Xu, W. / Jalomo-Khayrova, E. / Gumerov, V.M. / Ross, P.A. / Kobel, T.S. / Schindler, D. / Bange, G. / Zhulin, I.B. / Sourjik, V.
History
DepositionDec 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cache domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0934
Polymers33,8601
Non-polymers2333
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint4 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.000, 93.080, 44.380
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cache domain protein / Methyl-accepting chemotaxis protein McpC


Mass: 33859.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia intestinalis L1-82 (bacteria)
Gene: mcpC_1, RIL182_00127, ROSINTL182_06964 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: C7GAN4
#2: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium fluoride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.46→46.54 Å / Num. obs: 48349 / % possible obs: 99.07 % / Redundancy: 6.8 % / Biso Wilson estimate: 10.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1673 / Rpim(I) all: 0.06886 / Net I/σ(I): 13.29
Reflection shellResolution: 1.464→1.516 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.9419 / Mean I/σ(I) obs: 3.31 / Num. unique obs: 4659 / CC1/2: 0.732 / Rpim(I) all: 0.3939 / % possible all: 95.55

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→46.54 Å / SU ML: 0.1544 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.8534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1889 2416 5 %
Rwork0.1681 45916 -
obs0.1691 48332 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.83 Å2
Refinement stepCycle: LAST / Resolution: 1.46→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 16 265 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682376
X-RAY DIFFRACTIONf_angle_d0.89483243
X-RAY DIFFRACTIONf_chiral_restr0.0856360
X-RAY DIFFRACTIONf_plane_restr0.0066422
X-RAY DIFFRACTIONf_dihedral_angle_d5.3267337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.30111320.23662507X-RAY DIFFRACTION92.79
1.49-1.530.24011430.22682726X-RAY DIFFRACTION99.34
1.53-1.560.24271410.21762678X-RAY DIFFRACTION99.3
1.56-1.60.25941430.21172709X-RAY DIFFRACTION99.58
1.6-1.640.23731420.19142711X-RAY DIFFRACTION99.51
1.64-1.690.2061430.18312715X-RAY DIFFRACTION99.62
1.69-1.750.20821430.17722711X-RAY DIFFRACTION99.51
1.75-1.810.19481420.1692687X-RAY DIFFRACTION99.61
1.81-1.880.20911410.17262694X-RAY DIFFRACTION99.61
1.88-1.970.2051440.16842726X-RAY DIFFRACTION99.62
1.97-2.070.20311430.16562717X-RAY DIFFRACTION99.58
2.07-2.20.1821430.15652728X-RAY DIFFRACTION99.48
2.2-2.370.16881420.16162696X-RAY DIFFRACTION99.51
2.37-2.610.18661430.16482721X-RAY DIFFRACTION99.34
2.61-2.990.17951430.16992709X-RAY DIFFRACTION99.48
2.99-3.760.15921440.15052726X-RAY DIFFRACTION99.51
3.76-46.540.15041440.14412755X-RAY DIFFRACTION98.84

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