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- PDB-6is3: Crystal Structure of Staphylococcus aureus response regulator Arl... -

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Basic information

Entry
Database: PDB / ID: 6is3
TitleCrystal Structure of Staphylococcus aureus response regulator ArlR receiver domain
ComponentsResponse regulator ArlR
KeywordsSIGNALING PROTEIN / Staphylococcus aureus / response regulator / two-component regulatory system
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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 profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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
Response regulator ArlR
Similarity search - Component
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 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 1.2Mar 27, 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
C: Response regulator ArlR
A: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5824
Polymers29,3472
Non-polymers2352
Water3,999222
1
A: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8692
Polymers14,6741
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-10 kcal/mol
Surface area6650 Å2
MethodPISA
2
C: Response regulator ArlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7142
Polymers14,6741
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.375, 41.208, 42.877
Angle α, β, γ (deg.)97.50, 118.85, 96.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Response regulator ArlR


Mass: 14673.566 Da / Num. of mol.: 2 / Fragment: UNP residues 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus RF122 (bacteria) / Gene: arlR / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YY03
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Calcium chloride dehydrate, 0.1M MES and 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: 1.55→33 Å / Num. obs: 28417 / % possible obs: 87.26 % / Redundancy: 3.6 % / Net I/σ(I): 21.36
Reflection shellResolution: 1.55→1.6 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 / Resolution: 1.549→33 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 2000 7.04 %
Rwork0.1733 --
obs0.1756 28395 87.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.549→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 15 222 2188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082010
X-RAY DIFFRACTIONf_angle_d1.0242728
X-RAY DIFFRACTIONf_dihedral_angle_d13.5311235
X-RAY DIFFRACTIONf_chiral_restr0.059316
X-RAY DIFFRACTIONf_plane_restr0.006353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5493-1.5880.31751530.26082023X-RAY DIFFRACTION93
1.588-1.63090.25351530.23562020X-RAY DIFFRACTION94
1.6309-1.67890.24971550.20922039X-RAY DIFFRACTION95
1.6789-1.73310.22791550.21122056X-RAY DIFFRACTION95
1.7331-1.79510.24681580.2092079X-RAY DIFFRACTION95
1.7951-1.86690.24481540.20322032X-RAY DIFFRACTION95
1.8669-1.95190.3509890.22391178X-RAY DIFFRACTION91
1.9519-2.05480.23781120.18911482X-RAY DIFFRACTION95
2.0548-2.18350.19681570.18022072X-RAY DIFFRACTION96
2.1835-2.35210.1841950.16791247X-RAY DIFFRACTION58
2.3521-2.58870.23341610.17432128X-RAY DIFFRACTION97
2.5887-2.96320.22821590.18222090X-RAY DIFFRACTION97
2.9632-3.73270.20241490.16191964X-RAY DIFFRACTION91
3.7327-36.74060.14731500.14181985X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -5.2058 Å / Origin y: 9.4758 Å / Origin z: 8.0109 Å
111213212223313233
T0.1509 Å2-0.0085 Å2-0.0077 Å2-0.141 Å20.0293 Å2--0.1414 Å2
L0.8743 °2-0.3555 °2-0.1976 °2-2.0029 °21.2117 °2--1.2203 °2
S0.0489 Å °0.0424 Å °-0.0144 Å °0.0708 Å °-0.0652 Å °0.0245 Å °0.0176 Å °-0.062 Å °0.0259 Å °
Refinement TLS groupSelection details: all

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