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- PDB-3atp: Structure of the ligand binding domain of the bacterial serine ch... -

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Basic information

Entry
Database: PDB / ID: 3atp
TitleStructure of the ligand binding domain of the bacterial serine chemoreceptor Tsr with ligand
ComponentsMethyl-accepting chemotaxis protein I
KeywordsSIGNALING PROTEIN / Chemoreceptor / serine biniding / membrane
Function / homology
Function and homology information


regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cell motility / cellular response to amino acid stimulus / chemotaxis ...regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cell motility / cellular response to amino acid stimulus / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Aspartate receptor, ligand-binding domain / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain ...Aspartate receptor, ligand-binding domain / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / 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). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
SERINE / Methyl-accepting chemotaxis protein I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTajima, H. / Sakuma, M. / Homma, K. / Kawagishi, I. / Imada, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Ligand specificity determined by differentially arranged common ligand-binding residues in bacterial amino acid chemoreceptors Tsr and Tar.
Authors: Tajima, H. / Imada, K. / Sakuma, M. / Hattori, F. / Nara, T. / Kamo, N. / Homma, M. / Kawagishi, I.
History
DepositionJan 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 protein I
B: Methyl-accepting chemotaxis protein I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2504
Polymers38,0402
Non-polymers2102
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-8 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.972, 133.737, 39.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Methyl-accepting chemotaxis protein I / MCP-I / Serine chemoreceptor protein


Mass: 19019.967 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. W3110 / Gene: tsr, cheD, b4355, JW4318 / Plasmid: pIQ301 / Production host: Escherichia coli (E. coli) / Strain (production host): HCB436 / References: UniProt: P02942
#2: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.81 Å3/Da / Density % sol: 31.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12-14% PEG 1000, 0.1M Acetate buffer, 80-100mM ammonium acetate , pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 35 K / Ambient temp details: He-gas flow cryo-cooling system
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2004
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.5 Å / Num. all: 9819 / Num. obs: 9819 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 85.2 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 16.7
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1447 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.57 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1560008.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 981 10 %RANDOM
Rwork0.258 ---
obs0.258 9805 97.1 %-
all-9805 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9539 Å2 / ksol: 0.298546 e/Å3
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1--18.64 Å20 Å20 Å2
2--36.74 Å20 Å2
3----18.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 14 59 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 160 9.8 %
Rwork0.385 1470 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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