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- PDB-4k08: Periplasmic sensor domain of chemotaxis protein, Adeh_3718 -

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Basic information

Entry
Database: PDB / ID: 4k08
TitlePeriplasmic sensor domain of chemotaxis protein, Adeh_3718
ComponentsMethyl-accepting chemotaxis sensory transducer
KeywordsSIGNALING PROTEIN / methyl accepting chemotaxis / Anaeromyxobacter dehalogenans / PAS-like sensor domain / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / periplasmic sensor domain
Function / homology
Function and homology information


membrane => GO:0016020 / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Double Cache domain 2 / Cache domain / Single Cache domain 2 / Cache_2 / 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 ...Double Cache domain 2 / Cache domain / Single Cache domain 2 / Cache_2 / 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 / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Methyl-accepting chemotaxis sensory transducer
Similarity search - Component
Biological speciesAnaeromyxobacter dehalogenans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPokkuluri, P.R. / Mack, J.C. / Bearden, J. / Rakowski, E. / Schiffer, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Microbiologyopen / Year: 2013
Title: Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: structure of one sensor domain from a histidine kinase and another from a chemotaxis protein.
Authors: Pokkuluri, P.R. / Dwulit-Smith, J. / Duke, N.E. / Wilton, R. / Mack, J.C. / Bearden, J. / Rakowski, E. / Babnigg, G. / Szurmant, H. / Joachimiak, A. / Schiffer, M.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4413
Polymers17,3171
Non-polymers1242
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Methyl-accepting chemotaxis sensory transducer
hetero molecules

A: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8836
Polymers34,6342
Non-polymers2494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2250 Å2
ΔGint-89 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.595, 50.595, 112.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Methyl-accepting chemotaxis sensory transducer


Mass: 17317.023 Da / Num. of mol.: 1 / Fragment: Periplasmic sensor domain (UNP residues 38-190)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaeromyxobacter dehalogenans (bacteria)
Strain: 2CP-C / Gene: Adeh_3718 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IFX2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Membfac-2 (12% PEG4000, 0.1M sodium acetate pH 4.6, 0.1 M zinc acetate) diluted by water; (membfac-2, 350 uL + water, 150 uL), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
DetectorDetector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 21845 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 53
Reflection shellResolution: 2→2.02 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→34.594 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 21.3 / Stereochemistry target values: MLHL / Details: Hydrogens were added in the riding positions
RfactorNum. reflection% reflection
Rfree0.2377 1037 4.76 %
Rwork0.1953 --
obs0.1972 21799 99.91 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.13 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1087 Å2-0 Å20 Å2
2---2.1087 Å2-0 Å2
3---4.2174 Å2
Refinement stepCycle: LAST / Resolution: 2→34.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 5 76 1202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191180
X-RAY DIFFRACTIONf_angle_d1.6751603
X-RAY DIFFRACTIONf_dihedral_angle_d14.421430
X-RAY DIFFRACTIONf_chiral_restr0.095165
X-RAY DIFFRACTIONf_plane_restr0.008214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10560.28641480.23482986X-RAY DIFFRACTION100
2.1056-2.23750.29021650.22572901X-RAY DIFFRACTION100
2.2375-2.41020.25681680.19572998X-RAY DIFFRACTION100
2.4102-2.65260.2311630.19842952X-RAY DIFFRACTION100
2.6526-3.03630.27411190.18342966X-RAY DIFFRACTION100
3.0363-3.82460.23521380.18622978X-RAY DIFFRACTION100
3.8246-34.5990.20211360.19272981X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17350.165-0.55633.80820.21333.5337-0.14460.2946-0.4766-0.37350.00140.63070.4816-0.6357-0.08270.3012-0.1380.06490.357-0.07660.40592.477818.4851.8602
21.959-0.2559-0.41391.1006-0.19042.3438-0.0654-0.0592-0.65340.6040.29150.45220.28540.020.70790.32370.07390.3550.17530.08560.18959.781320.472614.3858
31.82431.1885-0.99650.9166-0.66641.065-0.10480.0627-0.29540.28710.0360.51530.2134-0.6110.08770.35180.02720.35450.38310.11470.6354-4.079220.11417.9493
41.219-0.5482-0.45081.67180.03121.9357-0.17260.1475-0.24420.17260.18520.3650.0343-0.4211-0.0380.26260.03870.17080.27470.05260.3842.743425.670711.3681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 38:68)
2X-RAY DIFFRACTION2chain 'A' and (resseq 69:128)
3X-RAY DIFFRACTION3chain 'A' and (resseq 129:140)
4X-RAY DIFFRACTION4chain 'A' and (resseq 141:181)

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