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- PDB-1qu7: FOUR HELICAL-BUNDLE STRUCTURE OF THE CYTOPLASMIC DOMAIN OF A SERI... -

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Basic information

Entry
Database: PDB / ID: 1qu7
TitleFOUR HELICAL-BUNDLE STRUCTURE OF THE CYTOPLASMIC DOMAIN OF A SERINE CHEMOTAXIS RECEPTOR
ComponentsMETHYL-ACCEPTING CHEMOTAXIS PROTEIN I
KeywordsSIGNALING PROTEIN / SERINE / CHEMOTAXIS / FOUR HELICAL-BUNDLE
Function / homology
Function and homology information


: / detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein trimerization / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cellular response to amino acid stimulus / cell motility ...: / detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein trimerization / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cellular response to amino acid stimulus / cell motility / protein homooligomerization / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Methyl-accepting chemotaxis protein / 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 / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKim, K.K. / Yokota, H. / Kim, S.-H.
CitationJournal: Nature / Year: 1999
Title: Four-helical-bundle structure of the cytoplasmic domain of a serine chemotaxis receptor.
Authors: Kim, K.K. / Yokota, H. / Kim, S.H.
History
DepositionJul 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYL-ACCEPTING CHEMOTAXIS PROTEIN I
B: METHYL-ACCEPTING CHEMOTAXIS PROTEIN I


Theoretical massNumber of molelcules
Total (without water)47,4832
Polymers47,4832
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-83 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.440, 132.440, 134.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein METHYL-ACCEPTING CHEMOTAXIS PROTEIN I


Mass: 23741.311 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN (RESIDUE 286-526)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: P02942
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 4.78 Å3/Da / Density % sol: 74.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: sparse matrix method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMEDTA11
225 mMHEPES11pH7.4
35-10 mg/ml11
40.1 MN-[2-acetamide]-2-iminodiacetic acid12pH6.5
515-20 %MPD12
60.2 Msodium citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 40467 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.84 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.745 / % possible all: 74
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0 / Redundancy: 3.84 % / Rmerge(I) obs: 0.125 / Biso Wilson estimate: 54.6 Å2
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.745

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 2.6→100 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: THE DISTRIBUTION OF THE INTENSITIES OF DIFFRACTION PATTERN WAS VERY ANISOTROPIC : 2.6 A ALONG C-AXIS, 3.5 A ALONG A,B AXIS. SINCE DIFFRACTION INTENSITIES ARE ANISOTROPIC, REFLECTIONS IN ...Details: THE DISTRIBUTION OF THE INTENSITIES OF DIFFRACTION PATTERN WAS VERY ANISOTROPIC : 2.6 A ALONG C-AXIS, 3.5 A ALONG A,B AXIS. SINCE DIFFRACTION INTENSITIES ARE ANISOTROPIC, REFLECTIONS IN RESOLUTION RANGE OF 30.0 - 3.5 A ALONG A AND B AXES, AND 2.6 A ALONG C-AXIS WERE USED FOR REFINEMENT.
RfactorNum. reflectionSelection details
Rfree0.276 1066 5 % RANDOM SELECTION
Rwork0.243 --
obs0.243 21860 -
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 0 187 3430
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.243 / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.51

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