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- PDB-3n0r: Structure of the PhyR stress response regulator at 1.25 Angstrom ... -

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Basic information

Entry
Database: PDB / ID: 3n0r
TitleStructure of the PhyR stress response regulator at 1.25 Angstrom resolution
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / sigma factor / receiver / response regulator / two-component signal transduction
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / PhyR, sigma-like (SL) domain / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / RNA polymerase sigma factor, region 3/4-like / Response regulator receiver domain ...Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / PhyR, sigma-like (SL) domain / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / RNA polymerase sigma factor, region 3/4-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 Å
AuthorsHerrou, J. / Crosson, S.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: A structural model of anti-anti-sigma inhibition by a two-component receiver domain: the PhyR stress response regulator
Authors: Herrou, J. / Foreman, R. / Fiebig, A. / Crosson, S.
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3232
Polymers31,2311
Non-polymers921
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.182, 61.198, 53.025
Angle α, β, γ (deg.)90.00, 108.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Response regulator


Mass: 31230.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Gene: CC_3477, PhyR / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9A2S9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 70 mM sodium acetate (pH 4.6), 20% glycerol (w/v), 16% PEG 600, 40 mM potassium phosphate , VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2010
RadiationMonochromator: Kohzu monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.25→28.6 Å / Num. all: 74275 / Num. obs: 73384 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 56.8
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 92.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: an unpublished model of Caulobacter crescentus PhyR solved by SAD to 1.6 Angstrom resolution.

Resolution: 1.251→28.38 Å / SU ML: 0.17 / Isotropic thermal model: anisotropic / σ(F): 0.18 / Phase error: 14.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1735 2000 2.83 %
Rwork0.1538 --
obs0.1544 70767 93.9 %
all-74275 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.886 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7817 Å2-0 Å20.1426 Å2
2---5.0426 Å20 Å2
3----2.7391 Å2
Refinement stepCycle: LAST / Resolution: 1.251→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 6 281 2260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052173
X-RAY DIFFRACTIONf_angle_d1.082984
X-RAY DIFFRACTIONf_dihedral_angle_d13.71842
X-RAY DIFFRACTIONf_chiral_restr0.074353
X-RAY DIFFRACTIONf_plane_restr0.005395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2512-1.29590.20441660.18075722X-RAY DIFFRACTION79
1.2959-1.34780.21621830.15536273X-RAY DIFFRACTION86
1.3478-1.40920.16161920.1346617X-RAY DIFFRACTION91
1.4092-1.48340.15921980.12076804X-RAY DIFFRACTION93
1.4834-1.57640.15162050.10777011X-RAY DIFFRACTION96
1.5764-1.69810.13792060.10857108X-RAY DIFFRACTION97
1.6981-1.86890.12712090.11577184X-RAY DIFFRACTION98
1.8689-2.13930.15242110.12447268X-RAY DIFFRACTION99
2.1393-2.6950.17232130.14867342X-RAY DIFFRACTION100
2.695-28.38740.1842170.16827438X-RAY DIFFRACTION100

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