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- PDB-5gpc: Structural analysis of fatty acid degradation regulator FadR from... -

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Basic information

Entry
Database: PDB / ID: 5gpc
TitleStructural analysis of fatty acid degradation regulator FadR from Bacillus halodurans
Components
  • DNA (5'-D(P*CP*AP*TP*GP*AP*AP*TP*GP*AP*GP*TP*AP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')
  • DNA (5'-D(P*GP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*AP*CP*TP*CP*AP*TP*TP*CP*AP*T)-3')
  • Transcriptional regulator (TetR/AcrR family)
KeywordsTRANSCRIPTION / DNA BINDING PROTEIN/DNA / fadR / transcriptional regulator / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Transcription regulator YsiA, C-terminal / YsiA-like protein, C-terminal region / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like ...Transcription regulator YsiA, C-terminal / YsiA-like protein, C-terminal region / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator (TetR/AcrR family)
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLee, J.Y. / Yeo, H.K. / Park, T.W.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Research Foundation of KoreaNRF; 2014R1A1A1A05008017 Korea, Republic Of
Agriculture Research CenterARC; 710003-03 Korea, Republic Of
Global PhD Fellowship programNRF-2011-0031110 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR.
Authors: Yeo, H.K. / Park, Y.W. / Lee, J.Y.
History
DepositionAug 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator (TetR/AcrR family)
B: Transcriptional regulator (TetR/AcrR family)
G: DNA (5'-D(P*CP*AP*TP*GP*AP*AP*TP*GP*AP*GP*TP*AP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')
C: Transcriptional regulator (TetR/AcrR family)
D: Transcriptional regulator (TetR/AcrR family)
E: DNA (5'-D(P*GP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*AP*CP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)102,0056
Polymers102,0056
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13460 Å2
ΔGint-126 kcal/mol
Surface area38380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.500, 76.935, 87.022
Angle α, β, γ (deg.)103.830, 105.480, 89.640
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transcriptional regulator (TetR/AcrR family)


Mass: 22280.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: BH3102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K8A4
#2: DNA chain DNA (5'-D(P*CP*AP*TP*GP*AP*AP*TP*GP*AP*GP*TP*AP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Mass: 6436.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*AP*CP*TP*CP*AP*TP*TP*CP*AP*T)-3')


Mass: 6445.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, PEG 8000, ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 26864 / % possible obs: 96.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 56.78 Å2 / Rmerge(I) obs: 0.101 / Net I/av σ(I): 13.985 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.8-2.8520.6080.603196.2
2.85-2.92.10.4920.715197.6
2.9-2.962.10.4220.786197.6
2.96-3.022.10.3840.877197.9
3.02-3.082.10.3370.822197.4
3.08-3.152.10.2880.889197.9
3.15-3.232.10.2350.926197.5
3.23-3.322.10.2020.952197.4
3.32-3.422.10.1620.975196.8
3.42-3.532.10.1270.985196.5
3.53-3.652.10.1310.97196
3.65-3.82.10.1180.966195.1
3.8-3.972.10.1010.975194.8
3.97-4.182.10.0880.983194.5
4.18-4.442.10.0770.988193.7
4.44-4.792.10.0720.989194.5
4.79-5.272.10.0680.985195.7
5.27-6.032.10.0650.987196.8
6.03-7.5920.0590.99197.5
7.59-501.90.0450.99194.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GP9

5gp9


Resolution: 2.8→19.904 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.97
RfactorNum. reflection% reflection
Rfree0.2656 1362 5.14 %
Rwork0.2049 --
obs0.2081 26518 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.67 Å2 / Biso mean: 51.9569 Å2 / Biso min: 18.24 Å2
Refinement stepCycle: final / Resolution: 2.8→19.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6081 861 0 17 6959
Biso mean---40.1 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047135
X-RAY DIFFRACTIONf_angle_d0.7739789
X-RAY DIFFRACTIONf_chiral_restr0.0281124
X-RAY DIFFRACTIONf_plane_restr0.0041095
X-RAY DIFFRACTIONf_dihedral_angle_d19.7652738
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.89980.42241520.32382483263594
2.8998-3.01550.3391500.30752511266197
3.0155-3.15230.33651370.26752544268198
3.1523-3.31770.34531120.24572616272897
3.3177-3.52450.28611260.21272504263096
3.5245-3.79490.27271360.20132513264995
3.7949-4.17370.26411380.18552467260595
4.1737-4.77030.23711250.17642467259294
4.7703-5.98290.25731410.18992528266996
5.9829-19.9050.19591450.1662523266897

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