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

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Basic information

Entry
Database: PDB / ID: 6kyx
TitleCrystal Structure of Staphylococcus aureus response regulator ArlR DNA binding domain with His tag cleaved
ComponentsDNA-binding response regulator ArlR
KeywordsDNA BINDING PROTEIN / bacterial signaling
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / cytosol
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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Response regulator ArlR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0048 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: To Be Published
Title: Crystal Structure of Staphylococcus aureus response regulator ArlR DNA binding domain
Authors: Wen, Y. / Ouyang, Z.
History
DepositionSep 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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
A: DNA-binding response regulator ArlR


Theoretical massNumber of molelcules
Total (without water)11,6771
Polymers11,6771
Non-polymers00
Water1,35175
1
A: DNA-binding response regulator ArlR

A: DNA-binding response regulator ArlR


Theoretical massNumber of molelcules
Total (without water)23,3552
Polymers23,3552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area2360 Å2
ΔGint-20 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.060, 68.060, 152.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-344-

HOH

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Components

#1: Protein DNA-binding response regulator ArlR


Mass: 11677.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ER627_12465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A482QZB9, UniProt: Q9KJN4*PLUS
#2: Water ChemComp-HOH / water / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.85 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 3.2 M Sodium chloride, 0.1 M Sodium acetate trihydrate pH 4.6

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→29.471 Å / Num. obs: 14804 / % possible obs: 99.7 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rsym value: 0.095 / Net I/σ(I): 21.05
Reflection shellResolution: 2→2.08 Å / Rmerge(I) obs: 1.18 / Num. unique obs: 2282 / CC1/2: 0.91

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.0048→29.471 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.9
Details: The scaled data used for the refinement was truncated with anisotropical server.
RfactorNum. reflection% reflection
Rfree0.2496 840 10.01 %
Rwork0.1995 --
obs0.2046 8388 56.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.38 Å2 / Biso mean: 31.3676 Å2 / Biso min: 8.25 Å2
Refinement stepCycle: final / Resolution: 2.0048→29.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 0 75 879
Biso mean---34.57 -
Num. residues----100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0048-2.13040.3999110.25581035
2.1304-2.29480.328370.267133015
2.2948-2.52560.289810.260373034
2.5256-2.89080.29061960.2516176881
2.8908-3.64110.25762480.20582224100
3.6411-29.4710.21882670.16392393100
Refinement TLS params.Method: refined / Origin x: -29.2883 Å / Origin y: -11.0858 Å / Origin z: -10.4422 Å
111213212223313233
T0.1588 Å20.0905 Å20.0088 Å2-0.1941 Å2-0.0091 Å2--0.07 Å2
L0.6465 °20.0967 °2-0.7633 °2-1.2178 °20.5062 °2--1.4702 °2
S0.0366 Å °0.0241 Å °-0.0331 Å °-0.1686 Å °-0.0699 Å °-0.1049 Å °0.2737 Å °0.2911 Å °-0.0193 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA120 - 219
2X-RAY DIFFRACTION1allS1 - 68
3X-RAY DIFFRACTION1allS69 - 75

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