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- PDB-2gkg: Receiver domain from Myxococcus xanthus social motility protein FrzS -

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Basic information

Entry
Database: PDB / ID: 2gkg
TitleReceiver domain from Myxococcus xanthus social motility protein FrzS
Componentsresponse regulator homolog
KeywordsSIGNALING PROTEIN / social motility / receiver domain / signalling / high resolution
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Response regulator homolog
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsEchols, N. / Fraser, J. / Merlie, J. / Zusman, D. / Alber, T.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
Authors: Fraser, J.S. / Merlie, J.P. / Echols, N. / Weisfield, S.R. / Mignot, T. / Wemmer, D.E. / Zusman, D.R. / Alber, T.
History
DepositionApr 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: response regulator homolog


Theoretical massNumber of molelcules
Total (without water)13,6871
Polymers13,6871
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.360, 64.360, 46.038
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsASU contains one copy of FrzS receiver domain. The full-length protein includes a coiled-coil domain and may oligomerize.

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Components

#1: Protein response regulator homolog


Mass: 13686.523 Da / Num. of mol.: 1 / Fragment: receiver domain (residues 1-124)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: FrzS / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 4063845, UniProt: O68522*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, NaFormate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.8856 / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1→20 Å / Num. all: 58567 / Num. obs: 58567 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.75
Reflection shellResolution: 1→1.02 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
EPMRphasing
SHELXL-97refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GUANYLATE CYCLASE RECEIVER DOMAIN (PDB CODE: 1W25)

1w25


Resolution: 1→20 Å / Num. parameters: 13613 / Num. restraintsaints: 18431 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: All hydrogen atoms on protein residues were included in the final round of refinement. Positions of hydroxyl and methyl hydrogens were refined independently.
RfactorNum. reflection% reflectionSelection details
Rfree0.1235 2999 5.12 %RANDOM
Rwork0.0916 ---
obs0.0916 58567 99.98 %-
all-58567 --
Refine analyzeNum. disordered residues: 31 / Occupancy sum hydrogen: 947 / Occupancy sum non hydrogen: 1204.95
Refinement stepCycle: LAST / Resolution: 1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 361 1283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0332
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.054
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.089

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