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- PDB-9bce: Shewanella oneidensis LysR family regulator SO0839 regulatory domain -

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Basic information

Entry
Database: PDB / ID: 9bce
TitleShewanella oneidensis LysR family regulator SO0839 regulatory domain
ComponentsTranscriptional regulator LysR family
KeywordsTRANSCRIPTION / regulator / acetyl-CoA / carboxylase
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator LysR family
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsHan, S.R. / Liang, H.H. / Lin, Z.H. / Fan, Y.L. / Ye, K. / Gao, H.G. / Tao, Y.J. / Jin, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)508104-N12002ZJ China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: A bacterial transcription activator dedicated to the expression of the enzyme catalyzing the first committed step in fatty acid biosynthesis.
Authors: Xu, Y. / Lin, Z. / Hou, J. / Ye, K. / Han, S. / Liang, Y. / Liang, H. / Wu, S. / Tao, Y.J. / Gao, H.
History
DepositionApr 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator LysR family
B: Transcriptional regulator LysR family


Theoretical massNumber of molelcules
Total (without water)47,9112
Polymers47,9112
Non-polymers00
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-8 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.040, 42.962, 112.092
Angle α, β, γ (deg.)90.00, 104.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

#1: Protein Transcriptional regulator LysR family


Mass: 23955.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_0839 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8EIK0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27.5% v/v PEG-4000 100 mM HEPES/ Sodium hydroxide, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 2019
RadiationMonochromator: 0.978 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 134465 / % possible obs: 94.81 % / Redundancy: 7.3 % / Biso Wilson estimate: 12.18 Å2 / Rmerge(I) obs: 0.1008 / Net I/σ(I): 12.41
Reflection shellResolution: 1.4→1.452 Å / Rpim(I) all: 0.1698 / Rsym value: 0.1958

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→39.01 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 4005 2.98 %
Rwork0.1698 --
obs0.1706 134465 84.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 0 502 3770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.026
X-RAY DIFFRACTIONf_dihedral_angle_d5.502494
X-RAY DIFFRACTIONf_chiral_restr0.087540
X-RAY DIFFRACTIONf_plane_restr0.008610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.3407200.3182659X-RAY DIFFRACTION
1.42-1.440.3545440.29281364X-RAY DIFFRACTION25
1.44-1.450.3644670.24562220X-RAY DIFFRACTION42
1.45-1.470.2794840.20242719X-RAY DIFFRACTION51
1.47-1.490.2223950.17783010X-RAY DIFFRACTION56
1.49-1.510.20211020.15883350X-RAY DIFFRACTION62
1.51-1.540.1951080.15613648X-RAY DIFFRACTION68
1.54-1.560.19911250.14963936X-RAY DIFFRACTION75
1.56-1.590.16111360.15014267X-RAY DIFFRACTION80
1.59-1.610.18521470.15254661X-RAY DIFFRACTION86
1.61-1.640.22191420.14974770X-RAY DIFFRACTION90
1.64-1.670.21261560.15175115X-RAY DIFFRACTION95
1.67-1.710.20281650.1615297X-RAY DIFFRACTION99
1.71-1.750.17721600.16095315X-RAY DIFFRACTION100
1.75-1.790.19551680.15965392X-RAY DIFFRACTION100
1.79-1.830.18411610.165260X-RAY DIFFRACTION100
1.83-1.880.1861620.15715349X-RAY DIFFRACTION100
1.88-1.940.15821655362X-RAY DIFFRACTION100
1.94-20.19271660.16215360X-RAY DIFFRACTION100
2-2.070.17271620.16365385X-RAY DIFFRACTION100
2.07-2.150.2031660.16245323X-RAY DIFFRACTION100
2.15-2.250.19881650.16855362X-RAY DIFFRACTION100
2.25-2.370.24371630.17835379X-RAY DIFFRACTION100
2.37-2.520.1841600.17935292X-RAY DIFFRACTION100
2.52-2.710.20751650.18975375X-RAY DIFFRACTION100
2.71-2.990.1771585287X-RAY DIFFRACTION100
2.99-3.420.20161680.17385376X-RAY DIFFRACTION100
3.42-4.30.15921675359X-RAY DIFFRACTION100
4.3-100.22731580.17285268X-RAY DIFFRACTION98

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