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- PDB-4xmr: Crystal structure of the sensory domain of the Campylobacter jeju... -

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Basic information

Entry
Database: PDB / ID: 4xmr
TitleCrystal structure of the sensory domain of the Campylobacter jejuni chemoreceptor Tlp3 (CcmL) with isoleucine bound.
ComponentsPutative methyl-accepting chemotaxis signal transduction protein
KeywordsSIGNALING PROTEIN / Sensory domain / chemotactic receptor / CcmL
Function / homology
Function and homology information


chemotaxis / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / 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).
Similarity search - Domain/homology
ISOLEUCINE / Methyl-accepting chemotaxis signal transduction protein
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsRoujeinikova, A. / Liu, Y.C. / Machuca, M.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains.
Authors: Liu, Y.C. / Machuca, M.A. / Beckham, S.A. / Gunzburg, M.J. / Roujeinikova, A.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyl-accepting chemotaxis signal transduction protein
B: Putative methyl-accepting chemotaxis signal transduction protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8556
Polymers57,4012
Non-polymers4544
Water14,412800
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-39 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.620, 138.010, 49.020
Angle α, β, γ (deg.)90.000, 94.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative methyl-accepting chemotaxis signal transduction protein


Mass: 28700.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) (Campylobacter)
Strain: NCTC 11168 / Gene: Cj1564 / Plasmid: pET151/D-Topo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q0P864
#2: Chemical ChemComp-ILE / ISOLEUCINE / Isoleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Ammonium sulfate, Isoleucine / PH range: Sodium Citrate pH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→39.89 Å / Num. obs: 128260 / % possible obs: 92.9 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Net I/σ(I): 12.2 / Num. measured all: 441329 / Scaling rejects: 158
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.3-1.322.60.3462.11046240460.830.26159.2
7.12-39.892.80.04821.410653750.9840.03442.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→26.997 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1729 6299 4.92 %RANDOM
Rwork0.1406 121611 --
obs0.1421 127910 92.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.78 Å2 / Biso mean: 22.85 Å2 / Biso min: 6.88 Å2
Refinement stepCycle: final / Resolution: 1.3→26.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 28 800 4787
Biso mean--42.46 34.03 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064313
X-RAY DIFFRACTIONf_angle_d1.0975890
X-RAY DIFFRACTIONf_chiral_restr0.077681
X-RAY DIFFRACTIONf_plane_restr0.005767
X-RAY DIFFRACTIONf_dihedral_angle_d11.9021625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31480.24991350.2262516265158
1.3148-1.33020.23751530.21672783293663
1.3302-1.34650.23331530.20732917307068
1.3465-1.36350.2451620.1953242340474
1.3635-1.38140.2261510.18063475362679
1.3814-1.40040.2012070.17253717392486
1.4004-1.42040.20682170.15724155437295
1.4204-1.44160.18842040.14844324452899
1.4416-1.46410.16052110.14294308451999
1.4641-1.48810.1812400.13354314455499
1.4881-1.51380.17332690.12924244451399
1.5138-1.54130.15282280.11744309453799
1.5413-1.57090.14632500.11414339458999
1.5709-1.6030.15482560.11214295455199
1.603-1.63780.15462430.11344385462899
1.6378-1.67590.15762280.11064270449899
1.6759-1.71780.16422130.119743774590100
1.7178-1.76430.15972470.120543704617100
1.7643-1.81620.17522360.120143504586100
1.8162-1.87480.14982060.121843924598100
1.8748-1.94180.16252130.121843854598100
1.9418-2.01950.14972170.120543674584100
2.0195-2.11140.14372060.119843924598100
2.1114-2.22260.1562200.12643664586100
2.2226-2.36180.1692250.131543764601100
2.3618-2.54410.18512200.143843354555100
2.5441-2.79980.17582500.150843554605100
2.7998-3.20440.18641700.150944364606100
3.2044-4.03510.17851920.1474190438295
4.0351-27.00280.19231770.18223327350475

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