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- PDB-2yfb: X-ray structure of McpS ligand binding domain in complex with suc... -

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Basic information

Entry
Database: PDB / ID: 2yfb
TitleX-ray structure of McpS ligand binding domain in complex with succinate
ComponentsMETHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
KeywordsRECEPTOR / CHEMORECEPTOR / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
de novo design (two linked rop proteins) - #210 / Helical bimodular sensor domain / Helical bimodular sensor domain / HBM domain profile. / helical bimodular (HBM) domain / Chemotaxis methyl-accepting receptor / de novo design (two linked rop proteins) / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. ...de novo design (two linked rop proteins) - #210 / Helical bimodular sensor domain / Helical bimodular sensor domain / HBM domain profile. / helical bimodular (HBM) domain / Chemotaxis methyl-accepting receptor / de novo design (two linked rop proteins) / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / SUCCINIC ACID / Methyl-accepting chemotaxis protein McpS
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGavira, J.A. / Pineda-Molina, E. / Krell, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Evidence for Chemoreceptors with Bimodular Ligand-Binding Regions Harboring Two Signal-Binding Sites.
Authors: Pineda-Molina, E. / Reyes-Darias, J. / Lacal, J. / Ramos, J.L. / Garcia-Ruiz, J.M. / Gavira, J.A. / Krell, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and Crystallographic Analysis of the Ligand-Binding Domain of the Pseudomonas Putida Chemoreceptor Mcps in Complex with Malate and Succinate.
Authors: Gavira, J.A. / Lacal, J. / Ramos, J.L. / Garcia-Ruiz, J.M. / Krell, T. / Pineda-Molina, E.
History
DepositionApr 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
B: METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9479
Polymers57,3042
Non-polymers6427
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-48.5 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.067, 46.039, 50.823
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER / MCPS


Mass: 28652.125 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 46-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: KT2440 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88E10
#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.63 Å3/Da / Density % sol: 53.22 % / Description: NONE
Crystal growpH: 5
Details: 20% PEG 4000, 0.25 M (NH4)2SO4 AND 100 MM SODIUM ACETATE, PH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 40558 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 27.34 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.97
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YFA

2yfa


Resolution: 1.9→19.911 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 1755 4.5 %
Rwork0.2041 --
obs0.2071 38883 93.96 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.677 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7791 Å20 Å20.8033 Å2
2--0.2223 Å20 Å2
3----1.0014 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 39 498 4202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073874
X-RAY DIFFRACTIONf_angle_d0.9425250
X-RAY DIFFRACTIONf_dihedral_angle_d17.0881528
X-RAY DIFFRACTIONf_chiral_restr0.061598
X-RAY DIFFRACTIONf_plane_restr0.004706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.34991180.272490X-RAY DIFFRACTION82
1.9514-2.00870.32291270.24752739X-RAY DIFFRACTION92
2.0087-2.07350.29111430.22752918X-RAY DIFFRACTION97
2.0735-2.14750.28361390.2092929X-RAY DIFFRACTION97
2.1475-2.23340.28651350.21512911X-RAY DIFFRACTION97
2.2334-2.33490.29551360.21772893X-RAY DIFFRACTION96
2.3349-2.45780.30531340.21432892X-RAY DIFFRACTION96
2.4578-2.61150.30161380.20922875X-RAY DIFFRACTION96
2.6115-2.81260.29031390.20912903X-RAY DIFFRACTION95
2.8126-3.09470.27421330.1982859X-RAY DIFFRACTION94
3.0947-3.54030.25331360.19722869X-RAY DIFFRACTION94
3.5403-4.45220.22621360.16412861X-RAY DIFFRACTION93
4.4522-19.91240.26881410.22262989X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.15850.0882-0.03460.33430.01520.31710.287-0.2439-0.01630.2324-0.3766-0.1945-0.09570.1195-0.03040.2388-0.0892-0.03430.19120.08630.163966.4090.517816.7457
20.41040.04420.22020.8127-0.52870.53970.1182-0.22790.31610.035-0.25670.1077-0.2241-0.0415-0.09250.1779-0.03230.00330.1312-0.02570.12843.98174.46189.6905
30.11770.02890.03330.2790.3740.36880.16140.01780.0888-0.1372-0.05860.26610.0276-0.2932-0.0350.1280.0042-0.01090.32290.07140.336115.2291-5.51875.9147
41.17830.77250.23170.6792-0.00811.0342-0.07870.28120.0017-0.15840.14030.27090.1957-0.21280.00970.1749-0.009-0.00450.28320.03510.22223.1665-2.1419-2.2815
50.26810.4323-0.18051.14110.12890.53170.21050.38680.13230.0134-0.205-0.12280.0096-0.01240.01270.1227-0.01880.00560.13370.09450.137949.56330.97974.3085
60.1775-0.3516-0.08130.35370.22730.09190.20890.23420.0247-0.1687-0.2186-0.10610.05180.0913-0.00820.17140.0490.04610.17750.06720.133968.6067-19.699610.717
71.1-0.3473-0.320.58-0.27060.2034-0.01360.0038-0.1728-0.01660.00280.1310.0428-0.0425-0.03260.1846-0.0364-0.00280.1521-0.00820.170534.3384-19.352616.3905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 43:99)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 100:157)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 158:191)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 192:223)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 224:277)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 40:99)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 100:277)

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