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- PDB-4zyl: Crystal structure of response regulator RPA3017 in red light sign... -

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Basic information

Entry
Database: PDB / ID: 4zyl
TitleCrystal structure of response regulator RPA3017 in red light signaling of R. palustris
ComponentsRphyB protein
KeywordsSIGNALING PROTEIN / response regulator / light signaling / two-component signaling
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
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsYang, X. / Moffat, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY024363 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structure of the response regulator RPA3017 involved in red-light signaling in Rhodopseudomonas palustris.
Authors: Yang, X. / Zeng, X. / Moffat, K. / Yang, X.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.4Mar 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RphyB protein
B: RphyB protein


Theoretical massNumber of molelcules
Total (without water)37,4782
Polymers37,4782
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-8 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.980, 60.980, 200.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein RphyB protein


Mass: 18739.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: rphyB, RPA3017 / Plasmid: pET24c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6N5G1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 60 % / Description: diamond
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium citrate tribasic, 0.1M sodium cacodylate pH6.5 and 4% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 17, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21308 / % possible obs: 99.3 % / Redundancy: 15 % / Net I/σ(I): 47

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→31.931 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1851 4.8 %
Rwork0.1885 --
obs0.1904 38580 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→31.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 0 75 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142368
X-RAY DIFFRACTIONf_angle_d1.3083233
X-RAY DIFFRACTIONf_dihedral_angle_d12.552859
X-RAY DIFFRACTIONf_chiral_restr0.083377
X-RAY DIFFRACTIONf_plane_restr0.007413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.30431340.29482762X-RAY DIFFRACTION96
1.8487-1.90310.27971160.26972842X-RAY DIFFRACTION100
1.9031-1.96450.24571720.22132831X-RAY DIFFRACTION100
1.9645-2.03470.24361250.20962849X-RAY DIFFRACTION100
2.0347-2.11620.2491470.19782817X-RAY DIFFRACTION100
2.1162-2.21250.18921280.19962836X-RAY DIFFRACTION100
2.2125-2.32910.22411400.18882871X-RAY DIFFRACTION100
2.3291-2.47490.24251540.21252828X-RAY DIFFRACTION100
2.4749-2.6660.22811570.21022848X-RAY DIFFRACTION100
2.666-2.93410.25661390.22182856X-RAY DIFFRACTION100
2.9341-3.35820.24091570.20742823X-RAY DIFFRACTION100
3.3582-4.22950.23421390.17522846X-RAY DIFFRACTION99
4.2295-31.93650.2011430.15182720X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.47210.1054-4.05575.38690.9088.10280.0856-0.640.12130.8866-0.34750.47890.39480.15290.12640.4584-0.10750.2070.2463-0.04150.290424.988582.8419-5.8324
27.3345-0.1075-4.25155.5937-0.7737.87370.11590.61750.0933-0.8821-0.3404-0.45930.3557-0.18180.12050.46310.10440.19940.24520.03560.303335.973682.7736-27.5013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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