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- PDB-6iot: The ligand binding domain of Mlp24 with arginine -

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Basic information

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


chemotaxis / 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
ARGININE / Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 20, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
C: Methyl-accepting chemotaxis protein
D: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,29012
Polymers114,4284
Non-polymers8618
Water1,45981
1
A: Methyl-accepting chemotaxis protein
D: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6456
Polymers57,2142
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-30 kcal/mol
Surface area22540 Å2
MethodPISA
2
B: Methyl-accepting chemotaxis protein
C: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6456
Polymers57,2142
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-30 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.530, 102.750, 93.410
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


Mass: 28607.121 Da / Num. of mol.: 4
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-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0, 45% (v/v) PEG 400, 0.1M calcium acetate

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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: RAYONIX MX225HE / Detector: CCD / Date: Apr 19, 2013
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.5 Å / Num. obs: 32455 / % possible obs: 97.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4264 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.483 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1689 5.21 %Random selection
Rwork0.2173 ---
obs0.2193 32398 96.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7511 0 52 81 7644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047700
X-RAY DIFFRACTIONf_angle_d1.00110444
X-RAY DIFFRACTIONf_dihedral_angle_d19.8852844
X-RAY DIFFRACTIONf_chiral_restr0.2661185
X-RAY DIFFRACTIONf_plane_restr0.0031354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.77950.2831600.24922490X-RAY DIFFRACTION96
2.7795-2.86920.35981350.24692512X-RAY DIFFRACTION96
2.8692-2.97170.31591470.25882517X-RAY DIFFRACTION96
2.9717-3.09070.28251200.25332579X-RAY DIFFRACTION96
3.0907-3.23130.31541280.24222560X-RAY DIFFRACTION96
3.2313-3.40170.27231450.22872545X-RAY DIFFRACTION97
3.4017-3.61470.23691500.21322526X-RAY DIFFRACTION97
3.6147-3.89370.25751590.21212561X-RAY DIFFRACTION97
3.8937-4.28530.22031340.19172585X-RAY DIFFRACTION97
4.2853-4.90490.19681410.17962586X-RAY DIFFRACTION98
4.9049-6.17770.25251210.21622607X-RAY DIFFRACTION98
6.1777-48.49050.23651490.21622641X-RAY DIFFRACTION97

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