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- PDB-6iov: The ligand binding domain of Mlp37 with arginine -

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Basic information

Entry
Database: PDB / ID: 6iov
TitleThe ligand binding domain of Mlp37 with arginine
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
ARGININE / 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: 2.351 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: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis of the binding affinity of chemoreceptors Mlp24p and Mlp37p for various amino acids.
Authors: Takahashi, Y. / Nishiyama, S.I. / Kawagishi, I. / Imada, K.
History
DepositionOct 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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)56,5974
Polymers56,2472
Non-polymers3502
Water2,108117
1
A: Methyl-accepting chemotaxis (MCP) signaling domain protein
hetero molecules

B: Methyl-accepting chemotaxis (MCP) signaling domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5974
Polymers56,2472
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area1210 Å2
ΔGint-12 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.593, 100.482, 106.806
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 / Methyl-accepting chemotaxis protein


Mass: 28123.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CGT79_04785, DN30_191 / Plasmid: pGEX 6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A085T373, UniProt: Q9KL26*PLUS
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 2.0M ammonium sulfate, 1.2% (v/v) PEG 400

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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 2, 2015
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→47.2 Å / Num. obs: 22612 / % possible obs: 98.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2141 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AVE

5ave


Resolution: 2.351→47.157 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1999 8.86 %Random selection
Rwork0.1852 ---
obs0.1903 22568 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.351→47.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 24 117 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093533
X-RAY DIFFRACTIONf_angle_d1.0754815
X-RAY DIFFRACTIONf_dihedral_angle_d14.8311275
X-RAY DIFFRACTIONf_chiral_restr0.043547
X-RAY DIFFRACTIONf_plane_restr0.006629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3512-2.410.26821330.20911391X-RAY DIFFRACTION97
2.41-2.47510.29171410.20331476X-RAY DIFFRACTION99
2.4751-2.5480.23581380.19841399X-RAY DIFFRACTION96
2.548-2.63020.31411310.20541445X-RAY DIFFRACTION98
2.6302-2.72420.27541530.19641451X-RAY DIFFRACTION99
2.7242-2.83320.27071390.21221445X-RAY DIFFRACTION99
2.8332-2.96220.25551390.21011486X-RAY DIFFRACTION99
2.9622-3.11830.27751450.20711470X-RAY DIFFRACTION100
3.1183-3.31360.26841420.19661451X-RAY DIFFRACTION98
3.3136-3.56940.25141400.18641468X-RAY DIFFRACTION98
3.5694-3.92840.22931510.16631479X-RAY DIFFRACTION100
3.9284-4.49650.21161440.15161514X-RAY DIFFRACTION100
4.4965-5.66360.23371480.16661497X-RAY DIFFRACTION98
5.6636-47.16620.19071550.18371597X-RAY DIFFRACTION99

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