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- PDB-5g4y: Structural basis for carboxylic acid recognition by a Cache chemo... -

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Basic information

Entry
Database: PDB / ID: 5g4y
TitleStructural basis for carboxylic acid recognition by a Cache chemosensory domain.
ComponentsMethyl-accepting chemotaxis sensory transducer with Cache sensor
KeywordsSIGNALING PROTEIN / CHEMOTAXIS / CHEMORECEPTORS / LIGAND BINDING DOMAINS / METHYL- ACCEPTING CHEMOTAXIS PROTEINS
Function / homology
Function and homology information


membrane => GO:0016020 / chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
Single Cache domain 2 / Single Cache domain 2 / Cache_2 / Chemotaxis methyl-accepting receptor / 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). / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain ...Single Cache domain 2 / Single Cache domain 2 / Cache_2 / Chemotaxis methyl-accepting receptor / 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). / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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
Unknown ligand / Methyl-accepting chemotaxis sensory transducer with Cache sensor
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrewster, J. / McKellar, J.L.O. / Newman, J. / Peat, T.S. / Gerth, M.L.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae.
Authors: Brewster, J.L. / McKellar, J.L. / Finn, T.J. / Newman, J. / Peat, T.S. / Gerth, M.L.
History
DepositionMay 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_PDB_id_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Jan 10, 2024Group: 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 sensory transducer with Cache sensor


Theoretical massNumber of molelcules
Total (without water)20,1832
Polymers20,1831
Non-polymers01
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.282, 74.282, 75.057
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Methyl-accepting chemotaxis sensory transducer with Cache sensor


Mass: 20182.893 Da / Num. of mol.: 1 / Fragment: C2-CHEMORECEPTOR SENSOR DOMAIN, RESIDUES 34-181
Source method: isolated from a genetically manipulated source
Details: MISSING N-TERMINAL DOMAIN / Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: BCD74_10458 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S3VA52
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL AND C-TERMINAL DOMAINS REMOVED. JUST THE CACHE C2 CHEMORECEPTOR SENSOR DOMAIN IS CRYSTALLIZED.

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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: 3.61 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PROTEIN AT 8.5 MG/ML IN 50 MM BIS-TRIS CHLORIDE, PH 6.5, 50 MM SODIUM CHLORIDE IN EQUAL VOLUME WITH 27% PEG 4000 AND 100 MM PROLINE AT 20 C IN SITTING DROPS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.8 Å / Num. obs: 16085 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.9 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K08

4k08


Resolution: 2→64.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.212 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY LIGAND IS ASSUMED TO BE PROPIONATE AS THAT FITS THE DENSITY WELL, BUT NO PROPIONATE WAS ADDED TO THE PROTEIN OR CRYSTALS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18315 840 5.2 %RANDOM
Rwork0.1607 ---
obs0.16196 15217 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.557 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20.76 Å20 Å2
2--1.52 Å2-0 Å2
3----4.92 Å2
Refinement stepCycle: LAST / Resolution: 2→64.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 5 81 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191222
X-RAY DIFFRACTIONr_bond_other_d0.0020.021149
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9431657
X-RAY DIFFRACTIONr_angle_other_deg1.04332651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37324.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44215208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.144155
X-RAY DIFFRACTIONr_chiral_restr0.1190.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211396
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.43.355597
X-RAY DIFFRACTIONr_mcbond_other3.4023.348596
X-RAY DIFFRACTIONr_mcangle_it4.4434.991748
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.123.738625
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 38 -
Rwork0.266 1135 -
obs--99.91 %

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