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- PDB-5brj: Structure of the bacteriophytochrome response regulator AtBRR -

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Basic information

Entry
Database: PDB / ID: 5brj
TitleStructure of the bacteriophytochrome response regulator AtBRR
ComponentsTwo component response regulator
KeywordsSIGNALING PROTEIN / bacteriophytochrome / response regulator / stable dimer / two component system
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesAgrobacterium tumefaciens CCNWGS0286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 Å
AuthorsBaker, A.W. / Satyshur, K.A. / Forest, K.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1256259 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008349-23 United States
CitationJournal: J.Bacteriol. / Year: 2016
Title: Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction.
Authors: Baker, A.W. / Satyshur, K.A. / Moreno Morales, N. / Forest, K.T.
History
DepositionMay 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Two component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8192
Polymers15,7951
Non-polymers241
Water2,432135
1
A: Two component response regulator
hetero molecules

A: Two component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6394
Polymers31,5902
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area3000 Å2
ΔGint-35 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.046, 41.046, 187.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

21A-378-

HOH

DetailsDimer confirmed by size exclusion chromatography and structure packing

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Components

#1: Protein Two component response regulator


Mass: 15795.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens CCNWGS0286 (bacteria)
Gene: ATCR1_17512 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G6XXW5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM magnesium chloride, 100 mM tris pH 8.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.92→35 Å / Num. obs: 13163 / % possible obs: 98.7 % / Redundancy: 27.2 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.072 / Net I/σ(I): 53.2
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 26.4 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 23 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692phasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RtBRR

Resolution: 1.922→30.896 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.41 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1296 10 %random
Rwork0.1956 ---
obs0.2002 12959 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.922→30.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 1 135 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071130
X-RAY DIFFRACTIONf_angle_d1.0291543
X-RAY DIFFRACTIONf_dihedral_angle_d12.781421
X-RAY DIFFRACTIONf_chiral_restr0.042184
X-RAY DIFFRACTIONf_plane_restr0.005201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9222-1.99920.27431370.21711243X-RAY DIFFRACTION97
1.9992-2.09010.28951400.21851258X-RAY DIFFRACTION98
2.0901-2.20030.30911370.22251240X-RAY DIFFRACTION98
2.2003-2.33810.28031410.21331263X-RAY DIFFRACTION99
2.3381-2.51860.29111430.21431283X-RAY DIFFRACTION99
2.5186-2.77190.271440.2191294X-RAY DIFFRACTION99
2.7719-3.17260.2471460.20691313X-RAY DIFFRACTION99
3.1726-3.99580.19261470.17461327X-RAY DIFFRACTION100
3.9958-30.89950.20711610.1731442X-RAY DIFFRACTION98

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