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- PDB-6is1: Crystal Structure of Staphylococcus aureus response regulator Arl... -

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Basic information

Entry
Database: PDB / ID: 6is1
TitleCrystal Structure of Staphylococcus aureus response regulator ArlR receiver domain in complex with BeF3 and Mg
ComponentsResponse regulator ArlR
KeywordsSIGNALING PROTEIN / two-component regulatory system
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / IMIDAZOLE / Response regulator ArlR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsWen, Y. / Ouyang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNO.31870132, NO.81741088 and NO.31500051 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR.
Authors: Ouyang, Z. / Zheng, F. / Chew, J.Y. / Pei, Y. / Zhou, J. / Wen, K. / Han, M. / Lemieux, M.J. / Hwang, P.M. / Wen, Y.
History
DepositionNov 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 ArlR
C: Response regulator ArlR
B: Response regulator ArlR
D: Response regulator ArlR
E: Response regulator ArlR
F: Response regulator ArlR
G: Response regulator ArlR
H: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,12027
Polymers119,1908
Non-polymers93019
Water20,8791159
1
A: Response regulator ArlR
C: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9786
Polymers29,7982
Non-polymers1814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Response regulator ArlR
D: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0477
Polymers29,7982
Non-polymers2505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Response regulator ArlR
F: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0477
Polymers29,7982
Non-polymers2505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Response regulator ArlR
H: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0477
Polymers29,7982
Non-polymers2505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.112, 61.742, 66.063
Angle α, β, γ (deg.)90.36, 105.45, 92.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Response regulator ArlR


Mass: 14898.812 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: arlR, SAB1271c / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YY03
#2: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium fomate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.59→31.77 Å / Num. obs: 117259 / % possible obs: 93.68 % / Redundancy: 3.5 % / Net I/σ(I): 15.36
Reflection shellResolution: 1.59→1.65 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NNN

3nnn


Resolution: 1.59→31.77 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.95
RfactorNum. reflection% reflection
Rfree0.1894 2017 1.72 %
Rwork0.1587 --
obs0.1592 117191 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.59→31.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7793 0 55 1159 9007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018030
X-RAY DIFFRACTIONf_angle_d1.09410875
X-RAY DIFFRACTIONf_dihedral_angle_d12.4464924
X-RAY DIFFRACTIONf_chiral_restr0.0611257
X-RAY DIFFRACTIONf_plane_restr0.0071415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5899-1.62970.28980.245495X-RAY DIFFRACTION63
1.6297-1.67380.23291530.20578356X-RAY DIFFRACTION95
1.6738-1.7230.25891470.19998279X-RAY DIFFRACTION95
1.723-1.77860.22771440.2038373X-RAY DIFFRACTION95
1.7786-1.84220.22441450.18788409X-RAY DIFFRACTION95
1.8422-1.91590.23431450.17958408X-RAY DIFFRACTION96
1.9159-2.00310.22771500.17218397X-RAY DIFFRACTION96
2.0031-2.10870.19481510.16858442X-RAY DIFFRACTION96
2.1087-2.24080.20071340.1618410X-RAY DIFFRACTION96
2.2408-2.41370.18591480.15568492X-RAY DIFFRACTION97
2.4137-2.65650.20061530.16118559X-RAY DIFFRACTION97
2.6565-3.04070.16391530.15418533X-RAY DIFFRACTION97
3.0407-3.82990.17621480.13928569X-RAY DIFFRACTION97
3.8299-31.7780.15961480.13958452X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -6.4928 Å / Origin y: 16.2924 Å / Origin z: 14.6957 Å
111213212223313233
T0.0911 Å20.0007 Å2-0.0031 Å2-0.0984 Å20.0025 Å2--0.0993 Å2
L0.1125 °2-0.0133 °20.0124 °2-0.153 °20.0307 °2--0.1674 °2
S0.0052 Å °0.0153 Å °-0.005 Å °0.0019 Å °0.0019 Å °0.0059 Å °-0.0148 Å °0.011 Å °0 Å °
Refinement TLS groupSelection details: all

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