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- PDB-3oov: Crystal structure of a methyl-accepting chemotaxis protein, resid... -

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Basic information

Entry
Database: PDB / ID: 3oov
TitleCrystal structure of a methyl-accepting chemotaxis protein, residues 122 to 287
ComponentsMethyl-accepting chemotaxis protein, putative
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


plasma membrane => GO:0005886 / chemotaxis / transmembrane signaling receptor activity / signal transduction
Similarity search - Function
GAF domain / 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). / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily ...GAF domain / 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). / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GAF sensor methyl-accepting chemotaxis sensory transducer, class 40H
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoachimiak, A. / Duke, N.E.C. / Hatzos-Skintges, C. / Mulligan, R. / Clancy, S. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a methyl-accepting chemotaxis protein, residues 122 to 287
Authors: Joachimiak, A. / Duke, N.E.C. / Hatzos-Skintges, C. / Mulligan, R. / Clancy, S.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2017Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein, putative
B: Methyl-accepting chemotaxis protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6446
Polymers37,2762
Non-polymers3684
Water2,612145
1


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


Theoretical massNumber of molelcules
Total (without water)18,9144
Polymers18,6381
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Methyl-accepting chemotaxis protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7302
Polymers18,6381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.132, 60.132, 363.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-178-

HOH

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Components

#1: Protein Methyl-accepting chemotaxis protein, putative


Mass: 18637.951 Da / Num. of mol.: 2 / Fragment: residues 122-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU1704 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q74CG9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 10% w/v PEG 3000, 0.10M phosphate-citrate, pH4.2, 0.20M NaCl. (Wizard II, #36) cryoprotectant: included all of above, in addition to 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: double crystal Si(111) monochromator, focussing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→60.52 Å / Num. all: 21188 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 4.1 %

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→60.52 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.397 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30485 1073 5.1 %RANDOM
Rwork0.23681 ---
all0.24022 21188 --
obs0.24022 19859 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.315 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20.58 Å20 Å2
2--1.15 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 24 145 2674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222558
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.973462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4123.451113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78115431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.011524
X-RAY DIFFRACTIONr_chiral_restr0.1350.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211895
X-RAY DIFFRACTIONr_mcbond_it1.1791.51622
X-RAY DIFFRACTIONr_mcangle_it2.12822630
X-RAY DIFFRACTIONr_scbond_it3.5963936
X-RAY DIFFRACTIONr_scangle_it5.3084.5832
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 69 -
Rwork0.273 1305 -
obs--91.42 %

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