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- PDB-3g67: Crystal Structure of a Soluble Chemoreceptor from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3g67
TitleCrystal Structure of a Soluble Chemoreceptor from Thermotoga maritima
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / Four-helix bundle / methyl-accepting chemotaxis protein
Function / homology
Function and homology information


signal transduction / membrane
Similarity search - Function
Methyl-accepting chemotaxis protein / 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). / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.17 Å
AuthorsPollard, A.M. / Bilwes, A.M. / Crane, B.R.
CitationJournal: Biochemistry / Year: 2009
Title: The structure of a soluble chemoreceptor suggests a mechanism for propagating conformational signals.
Authors: Pollard, A.M. / Bilwes, A.M. / Crane, B.R.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Methyl-accepting chemotaxis protein


Theoretical massNumber of molelcules
Total (without water)48,2692
Polymers48,2692
Non-polymers00
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-97 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.712, 25.747, 119.610
Angle α, β, γ (deg.)90.00, 93.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


Mass: 24134.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: Tm0014, TM_0014 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): B21 (DE3) / References: UniProt: Q7DFA3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.19 Å3/Da / Density % sol: 43.76 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.48
SYNCHROTRONCHESS F220.9479
Detector
TypeIDDetector
RIGAKU RAXIS1IMAGE PLATE
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.481
20.94791
ReflectionResolution: 2.17→50 Å / Num. all: 70197 / Num. obs: 24221 / % possible obs: 96.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.236 / Rsym value: 0.061 / Net I/σ(I): 12.3
Reflection shellResolution: 2.17→2.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2198 / Rsym value: 0.236 / % possible all: 95.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.17→50 Å / σ(F): 2
RfactorNum. reflection
Rfree0.278 -
Rwork0.242 -
all-22985
obs-22562
Refinement stepCycle: LAST / Resolution: 2.17→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 653 4019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.973
X-RAY DIFFRACTIONc_mcangle_it3.008

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