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- PDB-2nt4: Receiver domain from Myxococcus xanthus social motility protein F... -

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Basic information

Entry
Database: PDB / ID: 2nt4
TitleReceiver domain from Myxococcus xanthus social motility protein FrzS (H92F mutant)
ComponentsResponse regulator homolog
KeywordsSIGNALING PROTEIN / social motility / signaling / receiver domain / two-component
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: 1.02 Å
AuthorsEchols, N. / Fraser, J. / Weisfield, S. / 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
DepositionNov 6, 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7312
Polymers13,6961
Non-polymers351
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.883, 37.119, 42.104
Angle α, β, γ (deg.)90.00, 102.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Response regulator homolog


Mass: 13695.551 Da / Num. of mol.: 1 / Fragment: Receiver domain / Mutation: H92F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: frzS / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21+ / References: UniProt: O68522
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM Bis-Tris pH 5.5, 25% PEG 3350, 20% MPD added before freezing, VAPOR DIFFUSION, SITTING 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.02→20 Å / Num. all: 51807 / Num. obs: 51807 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 14.3
Reflection shellResolution: 1.02→1.08 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2 / Num. unique all: 6553 / Rsym value: 0.327 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2gkg

2gkg


Resolution: 1.02→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.694 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.024 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1539 2625 5.1 %RANDOM
Rwork0.12253 ---
all0.1241 51778 --
obs0.1241 51778 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.37 Å2
2---0.05 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 1 246 1205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221109
X-RAY DIFFRACTIONr_bond_other_d0.0040.021019
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9871515
X-RAY DIFFRACTIONr_angle_other_deg0.84932391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.99625.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53515200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.626158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021310
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02214
X-RAY DIFFRACTIONr_nbd_refined0.2390.2230
X-RAY DIFFRACTIONr_nbd_other0.1860.21100
X-RAY DIFFRACTIONr_nbtor_refined0.170.2559
X-RAY DIFFRACTIONr_nbtor_other0.0820.2676
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.252
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1520.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6541.5922
X-RAY DIFFRACTIONr_mcbond_other0.5241.5289
X-RAY DIFFRACTIONr_mcangle_it2.01721161
X-RAY DIFFRACTIONr_scbond_it3.1563442
X-RAY DIFFRACTIONr_scangle_it4.3254.5354
X-RAY DIFFRACTIONr_rigid_bond_restr1.45732472
X-RAY DIFFRACTIONr_sphericity_free5.9383247
X-RAY DIFFRACTIONr_sphericity_bonded2.69732102
LS refinement shellResolution: 1.02→1.075 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.295 320 -
Rwork0.263 6009 -
obs-6329 81.63 %

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