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- PDB-4g97: Crystal structure of the response regulator PhyR from Brucella abortus -

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Basic information

Entry
Database: PDB / ID: 4g97
TitleCrystal structure of the response regulator PhyR from Brucella abortus
ComponentsResponse regulator receiver
KeywordsSIGNALING PROTEIN / response regulator / alfa + beta protein / response regulator of a two-component signal transduction system
Function / homology
Function and homology information


phosphorelay signal transduction system / host cell perinuclear region of cytoplasm / metal ion binding
Similarity search - Function
Signal transduction response regulator PhyR-like, alphaproteobacteria / PhyR, sigma-like (SL) domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Up-down Bundle ...Signal transduction response regulator PhyR-like, alphaproteobacteria / PhyR, sigma-like (SL) domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Response regulator receiver
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKlinke, S. / Sycz, G. / Rinaldi, J.J. / Paris, G. / Goldbaum, F.A.
CitationJournal: To be Published
Title: Crystal structure of the response regulator PhyR from Brucella abortus
Authors: Klinke, S. / Sycz, G. / Rinaldi, J.J. / Paris, G. / Goldbaum, F.A.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator receiver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9362
Polymers29,8961
Non-polymers401
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.370, 53.370, 177.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Response regulator receiver


Mass: 29895.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: BAB1_1671, BAB1_1671, PhyR / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q2YRH9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 22% PEG 4000, 11% ISOPROPANOL, 0.1 M SODIUM ACETATE, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 16947 / Num. obs: 16947 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.31 % / Biso Wilson estimate: 40.87 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 19.92
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 8.44 % / Rmerge(I) obs: 1.055 / Mean I/σ(I) obs: 1.87 / Num. unique all: 2641 / Rsym value: 1.055 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3N0R

3n0r


Resolution: 2.05→39.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9234 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 848 5.01 %RANDOM
Rwork0.2125 ---
all0.2143 16939 --
obs0.2143 16939 99.95 %-
Displacement parametersBiso mean: 45.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.963 Å20 Å20 Å2
2--3.963 Å20 Å2
3----7.9259 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.05→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 1 45 1870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011857HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092525HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d626SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes276HARMONIC5
X-RAY DIFFRACTIONt_it1857HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion17.31
X-RAY DIFFRACTIONt_chiral_improper_torsion260SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2229SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.17 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2675 133 5.03 %
Rwork0.2348 2509 -
all0.2366 2642 -
obs-2641 99.7 %

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