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- PDB-6ioq: The ligand binding domain of Mlp24 with glycine -

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Basic information

Entry
Database: PDB / ID: 6ioq
TitleThe ligand binding domain of Mlp24 with glycine
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / CHEMORECEPTOR / LIGAND COMPLEX / MCP-LIKE PROTEIN / PAS-LIKE DOMAIN
Function / homology
Function and homology information


membrane => GO:0016020 / chemotaxis / 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
GLYCINE / Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 Å
AuthorsTakahashi, Y. / Sumita, K. / Nishiyama, S. / Kawagishi, I. / Imada, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15H02386 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)23115008 Japan
Japan Society for the Promotion of Science17J02169 Japan
Japan Society for the Promotion of Science17KT0026 Japan
CitationJournal: J. Bacteriol. / Year: 2019
Title: Calcium Ions Modulate Amino Acid Sensing of the Chemoreceptor Mlp24 ofVibrio cholerae.
Authors: Takahashi, Y. / Nishiyama, S.I. / Sumita, K. / Kawagishi, I. / Imada, K.
History
DepositionOct 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7223
Polymers28,6071
Non-polymers1152
Water79344
1
A: Methyl-accepting chemotaxis protein
hetero molecules

A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4456
Polymers57,2142
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area1400 Å2
ΔGint-13 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.351, 64.637, 136.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

21A-637-

HOH

31A-641-

HOH

41A-644-

HOH

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Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 28607.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: mcpB_4, ERS013206_02812 / Plasmid: pGEX 6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H6VSA0, UniProt: Q9KQ43*PLUS
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 20% (w/v) PEG 8000, 0.2M magnesium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→41.6 Å / Num. obs: 25096 / % possible obs: 98.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.7
Reflection shellResolution: 2.14→2.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3 / Num. unique obs: 3946 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.143→41.599 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 676 5.01 %Random selection
Rwork0.1955 ---
obs0.198 13505 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.143→41.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 6 44 1900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081890
X-RAY DIFFRACTIONf_angle_d1.0672564
X-RAY DIFFRACTIONf_dihedral_angle_d13.255695
X-RAY DIFFRACTIONf_chiral_restr0.045290
X-RAY DIFFRACTIONf_plane_restr0.004333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1435-2.3090.26941300.22872473X-RAY DIFFRACTION97
2.309-2.54130.2851340.22682540X-RAY DIFFRACTION100
2.5413-2.90890.28891350.2272560X-RAY DIFFRACTION100
2.9089-3.66460.23691360.19992584X-RAY DIFFRACTION100
3.6646-41.60690.2191410.16982672X-RAY DIFFRACTION99

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