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- PDB-5avf: The ligand binding domain of Mlp37 with taurine -

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Basic information

Entry
Database: PDB / ID: 5avf
TitleThe ligand binding domain of Mlp37 with taurine
ComponentsMethyl-accepting chemotaxis (MCP) signaling domain protein
KeywordsSIGNALING PROTEIN / chemoreceptor / ligand complex / MCP-like protein / PAS-like domain
Function / homology
Function and homology information


chemotaxis / membrane => GO:0016020 / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / 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 / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / 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 / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-AMINOETHANESULFONIC ACID / Methyl-accepting chemotaxis (MCP) signaling domain protein / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTakahashi, Y. / Sumita, K. / Uchida, Y. / Nishiyama, S. / Kawagishi, I. / Imada, K.
CitationJournal: Sci Rep / Year: 2016
Title: Identification of a Vibrio cholerae chemoreceptor that senses taurine and amino acids as attractants
Authors: Nishiyama, S. / Takahashi, Y. / Yamamoto, K. / Suzuki, D. / Itoh, Y. / Sumita, K. / Uchida, Y. / Homma, M. / Imada, K. / Kawagishi, I.
History
DepositionJun 15, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 (MCP) signaling domain protein
B: Methyl-accepting chemotaxis (MCP) signaling domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5854
Polymers56,3352
Non-polymers2502
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-11 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.230, 119.050, 138.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methyl-accepting chemotaxis (MCP) signaling domain protein


Mass: 28167.406 Da / Num. of mol.: 2 / Fragment: UNP residues 30-275
Source method: isolated from a genetically manipulated source
Details: A periplasmic fragment (58-303) of Mlp37. N-terminal GPLGS, a remnant of the GST-tag; C-terminal His x 6
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: DN30_191 / Plasmid: pGEX 6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A085T373, UniProt: Q9KL26*PLUS
#2: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID / Taurine


Mass: 125.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 15% (w/v) PEG-8000 and 30% MPD

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→33.3 Å / Num. obs: 41301 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c8c

3c8c


Resolution: 1.95→32.316 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 2000 4.93 %Random selection
Rwork0.1933 ---
obs0.1955 40570 98.29 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.202 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.976 Å2-0 Å2-0 Å2
2---2.7619 Å20 Å2
3----3.2141 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 14 396 4148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083879
X-RAY DIFFRACTIONf_angle_d1.0345296
X-RAY DIFFRACTIONf_dihedral_angle_d15.4461410
X-RAY DIFFRACTIONf_chiral_restr0.07600
X-RAY DIFFRACTIONf_plane_restr0.005697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.31631340.22272584X-RAY DIFFRACTION95
1.9988-2.05280.24121380.21522657X-RAY DIFFRACTION96
2.0528-2.11320.25711370.20992648X-RAY DIFFRACTION96
2.1132-2.18140.26881380.19922678X-RAY DIFFRACTION98
2.1814-2.25930.27441420.19592729X-RAY DIFFRACTION98
2.2593-2.34980.25861410.19912728X-RAY DIFFRACTION98
2.3498-2.45670.26681410.20232713X-RAY DIFFRACTION99
2.4567-2.58610.25271440.20542782X-RAY DIFFRACTION99
2.5861-2.74810.25651440.21092770X-RAY DIFFRACTION99
2.7481-2.96010.23921440.20142771X-RAY DIFFRACTION99
2.9601-3.25780.27581460.19872799X-RAY DIFFRACTION100
3.2578-3.72860.22951470.17332840X-RAY DIFFRACTION100
3.7286-4.69530.16511480.1612867X-RAY DIFFRACTION100
4.6953-32.32050.22341560.20023004X-RAY DIFFRACTION99

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