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- PDB-6k8e: Global regulatory element SarX -

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Basic information

Entry
Database: PDB / ID: 6k8e
TitleGlobal regulatory element SarX
ComponentsHTH-type transcriptional regulator SarX
KeywordsTRANSCRIPTION / Global regulatory element / DNA-binding / transcriptional contral
Function / homologyTranscriptional regulator SarA/Rot / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / regulation of DNA-templated transcription / DNA binding / cytoplasm / HTH-type transcriptional regulator SarX
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsWang, Q.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31130018 China
National Natural Science Foundation of China31370732 China
National Natural Science Foundation of China31270014 China
National Natural Science Foundation of ChinaU1432107 China
CitationJournal: To Be Published
Title: Crystal structure of SarX from Staphylococcus aureus
Authors: Wang, Q.
History
DepositionJun 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: HTH-type transcriptional regulator SarX
D: HTH-type transcriptional regulator SarX


Theoretical massNumber of molelcules
Total (without water)30,6122
Polymers30,6122
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, SarX proteins could be cross-linked into homodimers in solution environment
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-8 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.405, 33.405, 231.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein HTH-type transcriptional regulator SarX / Staphylococcal accessory regulator X


Mass: 15305.761 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Gene: sarX, SAOUHSC_00674 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q2G0D1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1M Bicine pH 9.0, 2% 1,4-Dioxane, 10% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17045 / % possible obs: 99.99 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 19.26
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 1745 / Rsym value: 0.597 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HS5

5hs5


Resolution: 2.002→33.405 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.01
RfactorNum. reflection% reflection
Rfree0.2662 856 5.05 %
Rwork0.2168 --
obs0.2193 16940 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→33.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 0 53 1944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071913
X-RAY DIFFRACTIONf_angle_d0.9762554
X-RAY DIFFRACTIONf_dihedral_angle_d13.878758
X-RAY DIFFRACTIONf_chiral_restr0.072293
X-RAY DIFFRACTIONf_plane_restr0.003314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.12740.30731450.24842688X-RAY DIFFRACTION100
2.1274-2.29160.32111340.24832670X-RAY DIFFRACTION100
2.2916-2.52220.34621320.25952696X-RAY DIFFRACTION100
2.5222-2.8870.29921590.2562655X-RAY DIFFRACTION100
2.887-3.63660.28291460.2342693X-RAY DIFFRACTION100
3.6366-33.40960.22181400.18412682X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.2534 Å / Origin y: 12.4363 Å / Origin z: 16.9006 Å
111213212223313233
T0.2688 Å20.0109 Å20.0024 Å2-0.2964 Å2-0.0029 Å2--0.3915 Å2
L0.8039 °20.2333 °20.9199 °2-0.9714 °2-0.9181 °2--8.3773 °2
S-0.0265 Å °0.1795 Å °-0.0975 Å °0.1635 Å °-0.0095 Å °0.0758 Å °-0.3741 Å °0.3513 Å °0.0279 Å °
Refinement TLS groupSelection details: all

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