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- PDB-5ave: The ligand binding domain of Mlp37 with serine -

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Basic information

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


membrane => GO:0016020 / signal transduction / 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
SERINE / 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: 1.8 Å
AuthorsTakahashi, Y. / Sumita, K. / Uchida, Y. / Nishiyama, S. / Kawagishi, I. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
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 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 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 1.2Mar 20, 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 (MCP) signaling domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2722
Polymers28,1671
Non-polymers1051
Water3,711206
1
A: Methyl-accepting chemotaxis (MCP) signaling domain protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,5454
Polymers56,3352
Non-polymers2102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1590 Å2
ΔGint-15 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.720, 134.220, 50.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

21A-793-

HOH

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Components

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


Mass: 28167.406 Da / Num. of mol.: 1 / 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: A0A0H3AES3*PLUS
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M Phosphate-citrate pH 4.2, 10% (w/v) PEG-8000 and 0.2M NaCl

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Data collection

DiffractionMean temperature: 95 K / Ambient temp details: helical scan
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 19, 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: 1.8→31.721 Å / Num. obs: 31377 / % possible obs: 99.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 4.7 / % possible all: 99.2

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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 / Resolution: 1.8→31.721 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.86 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 1583 5.05 %Random selection
Rwork0.1876 ---
obs0.1889 31367 99.34 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.767 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0356 Å2-0 Å20 Å2
2---1.5171 Å2-0 Å2
3---2.5527 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 7 206 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062025
X-RAY DIFFRACTIONf_angle_d1.0082761
X-RAY DIFFRACTIONf_dihedral_angle_d12.9739
X-RAY DIFFRACTIONf_chiral_restr0.072313
X-RAY DIFFRACTIONf_plane_restr0.004361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.31571600.26052650X-RAY DIFFRACTION99
1.8581-1.92450.29041330.22072664X-RAY DIFFRACTION99
1.9245-2.00160.21671280.19612679X-RAY DIFFRACTION99
2.0016-2.09260.2171440.18482680X-RAY DIFFRACTION99
2.0926-2.20290.21831460.18772687X-RAY DIFFRACTION99
2.2029-2.34090.21761370.18652683X-RAY DIFFRACTION100
2.3409-2.52160.22091500.19052722X-RAY DIFFRACTION100
2.5216-2.77520.24941370.19782728X-RAY DIFFRACTION100
2.7752-3.17650.23181530.20212719X-RAY DIFFRACTION100
3.1765-4.00080.18761390.1792763X-RAY DIFFRACTION100
4.0008-31.72540.17911560.16522809X-RAY DIFFRACTION97

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