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- PDB-8py0: Sensor domain of Oscillibacter ruminantium chemoreceptor in compl... -

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Basic information

Entry
Database: PDB / ID: 8py0
TitleSensor domain of Oscillibacter ruminantium chemoreceptor in complex with formate.
ComponentsLigand Binding domain (LBD) Chemoreceptor
KeywordsSIGNALING PROTEIN / chemotaxis / chemoreceptor / Oscillibacter ruminantium
Function / homologyFORMIC ACID
Function and homology information
Biological speciesOscillibacter ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGavira, J.A. / Krell, T. / Monteagudo-Cascales, E. / Velando, F. / Matilla, M.A. / Martinez-Rodriguez, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-112612GB-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2020-116261GB-I00 Spain
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Bacterial sensor evolved by decreasing complexity.
Authors: Monteagudo-Cascales, E. / Gavira, J.A. / Xing, J. / Velando, F. / Matilla, M.A. / Zhulin, I.B. / Krell, T.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ligand Binding domain (LBD) Chemoreceptor
B: Ligand Binding domain (LBD) Chemoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3596
Polymers40,2212
Non-polymers1384
Water4,504250
1
A: Ligand Binding domain (LBD) Chemoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1793
Polymers20,1101
Non-polymers692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ligand Binding domain (LBD) Chemoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1793
Polymers20,1101
Non-polymers692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.379, 58.379, 156.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ligand Binding domain (LBD) Chemoreceptor


Mass: 20110.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillibacter ruminantium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.82 Å3/Da / Density % sol: 32.44 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.2
Details: 10% (w/v) PEG 8000, 100 mM Potassium phosphate monobasic/ Sodium phosphate dibasic pH 6.2, 200 mM Sodium chloride
PH range: 5.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.75→50.56 Å / Num. obs: 31411 / % possible obs: 97.8 % / Redundancy: 4.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.092 / Rrim(I) all: 0.205 / Χ2: 0.58 / Net I/σ(I): 5.9 / Num. measured all: 150638
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 1.444 / Num. measured all: 8664 / Num. unique obs: 1719 / CC1/2: 0.572 / Rpim(I) all: 0.706 / Rrim(I) all: 1.612 / Χ2: 0.57 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→50.56 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1535 4.94 %
Rwork0.1883 --
obs0.1897 31065 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→50.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 8 250 2581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.697
X-RAY DIFFRACTIONf_dihedral_angle_d6.08406
X-RAY DIFFRACTIONf_chiral_restr0.045413
X-RAY DIFFRACTIONf_plane_restr0.009507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.28881510.27812716X-RAY DIFFRACTION100
1.81-1.870.27781880.24522668X-RAY DIFFRACTION100
1.87-1.950.36921100.29032407X-RAY DIFFRACTION88
1.95-2.030.25731370.21922732X-RAY DIFFRACTION100
2.03-2.140.23241330.18712733X-RAY DIFFRACTION100
2.14-2.280.21161000.19342331X-RAY DIFFRACTION84
2.28-2.450.21331730.18442734X-RAY DIFFRACTION100
2.45-2.70.20981270.18522771X-RAY DIFFRACTION100
2.7-3.090.2251280.18332806X-RAY DIFFRACTION100
3.09-3.890.17631400.16542703X-RAY DIFFRACTION95
3.89-50.560.18861480.16422929X-RAY DIFFRACTION99
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)
10.6788-0.17130.0770.3877-0.03840.25560.02460.03350.07550.03550.0012-0.02440.01230.08570.10870.06390.0141-0.00120.17140.0050.0964-0.4781-26.5488-11.9449
20.51130.313-0.05470.41050.08170.43060.04990.13570.0346-0.1822-0.03070.12610.0134-0.33780.00580.0231-0.01230.00340.27840.00430.08560.5424-23.4019-40.4702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 34 through 188)
2X-RAY DIFFRACTION2(chain 'B' and resid 34 through 190)

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