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- PDB-4z9i: Asp-TarS from E. coli -

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Basic information

Entry
Database: PDB / ID: 4z9i
TitleAsp-TarS from E. coli
ComponentsMethyl-accepting chemotaxis protein II
KeywordsPROTEIN BINDING / Bacterial chemotaxis / Aspartate receptor / Aspartate-binding protein
Function / homology
Function and homology information


detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / protein histidine kinase binding / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis ...detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / protein histidine kinase binding / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis / transmembrane signaling receptor activity / signal transduction / protein homodimerization activity / 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 ...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
ASPARTIC ACID / Methyl-accepting chemotaxis protein II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMise, T.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Analysis of the Ligand-Binding Domain of the Aspartate Receptor Tar from Escherichia coli
Authors: Mise, T.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 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 1.2Nov 8, 2023Group: 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 protein II
B: Methyl-accepting chemotaxis protein II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7013
Polymers44,5672
Non-polymers1331
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-10 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.460, 59.510, 79.380
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-accepting chemotaxis protein II / MCP-II / Aspartate chemoreceptor protein


Mass: 22283.730 Da / Num. of mol.: 2 / Fragment: UNP residues 26-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tar, cheM / Production host: Escherichia coli (E. coli) / References: UniProt: P07017
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: NaCl

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→42 Å / Num. obs: 52820 / % possible obs: 99.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.2
Reflection shellResolution: 1.57→1.65 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 6.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata scaling
MOLREPphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ASR

2asr


Resolution: 1.57→42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.236 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19849 2590 4.9 %RANDOM
Rwork0.16639 ---
obs0.16793 50227 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.735 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å2-0 Å2-0.04 Å2
2--0.21 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 9 280 2885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192650
X-RAY DIFFRACTIONr_bond_other_d0.0010.022457
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.9453573
X-RAY DIFFRACTIONr_angle_other_deg1.06235638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4215322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22824.745137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44615474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8221516
X-RAY DIFFRACTIONr_chiral_restr0.1730.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
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_it2.5522.0621297
X-RAY DIFFRACTIONr_mcbond_other2.5522.0621296
X-RAY DIFFRACTIONr_mcangle_it3.9043.0781616
X-RAY DIFFRACTIONr_mcangle_other3.9033.0771617
X-RAY DIFFRACTIONr_scbond_it3.9592.5041353
X-RAY DIFFRACTIONr_scbond_other3.9622.5061350
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9873.5921956
X-RAY DIFFRACTIONr_long_range_B_refined8.20818.0743459
X-RAY DIFFRACTIONr_long_range_B_other8.18817.9263416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.568→1.609 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 191 -
Rwork0.223 3612 -
obs--97.56 %

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