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- PDB-5tqj: Crystal structure of response regulator receiver protein from Bur... -

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Basic information

Entry
Database: PDB / ID: 5tqj
TitleCrystal structure of response regulator receiver protein from Burkholderia phymatum
ComponentsResponse regulator receiver protein
KeywordsSIGNALING PROTEIN / Burkholderia phymatum / regulator / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 receiver protein
Similarity search - Component
Biological speciesBurkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsEdwards, T.E. / Dranow, D.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of response regulator receiver protein from Burkholderia phymatum
Authors: Edwards, T.E. / Dranow, D.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionOct 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7715
Polymers14,6031
Non-polymers1684
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.600, 82.600, 31.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

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Components

#1: Protein Response regulator receiver protein


Mass: 14602.733 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phymatum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B2JEF9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BuphA.00051.a.B1.PS38011 at 14 mg/mL against MCSG1 screen condition C9, 0.8M LiCl, 0.1 M Tris pH 8.5, 32% PEG 4000 supplemented with 20% ethylene glycol as cryo protectant, crystal tracking ...Details: BuphA.00051.a.B1.PS38011 at 14 mg/mL against MCSG1 screen condition C9, 0.8M LiCl, 0.1 M Tris pH 8.5, 32% PEG 4000 supplemented with 20% ethylene glycol as cryo protectant, crystal tracking ID 284229c9, unique puck LBQ7-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 26700 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 9.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.3-1.330.4166.30.955191.7
1.33-1.370.357.50.968195.5
1.37-1.410.3058.530.976193.1
1.41-1.450.25510.080.983194.1
1.45-1.50.20512.530.989195.3
1.5-1.550.1615.520.991195
1.55-1.610.1417.550.994195.7
1.61-1.680.11920.240.996194.7
1.68-1.750.09724.240.997196.6
1.75-1.840.08227.470.998197.1
1.84-1.940.06932.610.998196.9
1.94-2.060.05937.390.998196.7
2.06-2.20.05141.910.999197.1
2.2-2.370.04745.350.999197.6
2.37-2.60.04448.120.999198.1
2.6-2.910.04350.720.999197.2
2.91-3.360.04154.090.999199.1
3.36-4.110.0455.790.997198.5
4.11-5.810.03955.390.999198.9
5.81-500.0450.870.999196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIX1.11rc3_2553refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NHZ

3nhz


Resolution: 1.3→36.94 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.98
RfactorNum. reflection% reflection
Rfree0.1715 2012 7.55 %
Rwork0.1384 --
obs0.1409 26662 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.95 Å2 / Biso mean: 14.208 Å2 / Biso min: 5.94 Å2
Refinement stepCycle: final / Resolution: 1.3→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 7 168 1094
Biso mean--32.05 26.3 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005996
X-RAY DIFFRACTIONf_angle_d0.8451373
X-RAY DIFFRACTIONf_chiral_restr0.075167
X-RAY DIFFRACTIONf_plane_restr0.005183
X-RAY DIFFRACTIONf_dihedral_angle_d16.926378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.33260.19861240.15771675179992
1.3326-1.36860.23141210.15111721184296
1.3686-1.40890.20981330.14821690182393
1.4089-1.45430.20121610.14061703186494
1.4543-1.50630.15711610.13341666182795
1.5063-1.56660.18241450.13051705185095
1.5666-1.63790.17181400.12881757189796
1.6379-1.72430.18411310.13211749188096
1.7243-1.83230.16161300.1261783191396
1.8323-1.97380.13451160.12751812192896
1.9738-2.17240.1461670.1251758192597
2.1724-2.48670.15471610.13781810197198
2.4867-3.13270.18761550.1471851200699
3.1327-36.95470.1741670.14531970213799

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