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- PDB-5gp9: Structural analysis of fatty acid degradation regulator FadR from... -

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Basic information

Entry
Database: PDB / ID: 5gp9
TitleStructural analysis of fatty acid degradation regulator FadR from Bacillus halodurans
ComponentsTranscriptional regulator (TetR/AcrR family)
KeywordsTRANSCRIPTION / DNA BINDING PROTEIN / fadR / transcriptional regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
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 ...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
PALMITIC ACID / Transcriptional regulator (TetR/AcrR family)
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.755 Å
AuthorsLee, J.Y. / Yeo, H.K. / Park, Y.W.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Research Foundation of Korea (NRF)NRF; 2014R1A1A1A05008017 Korea, Republic Of
Agriculture Research CenterARC; 710003-03 Korea, Republic Of
Global PhD FellowshipNRF; 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2837
Polymers44,5622
Non-polymers7215
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-29 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.873, 56.873, 200.884
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-403-

HOH

21B-424-

HOH

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Components

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


Mass: 22280.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 41.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl, MgCl2, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 38629 / % possible obs: 98.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.82 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Χ2: 2.024 / Net I/σ(I): 14 / Num. measured all: 291359
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.785.90.55616060.890.2390.6081.43283
1.78-1.817.10.518940.9120.1950.5381.47299.7
1.81-1.857.70.42819220.9410.1590.4581.57699.7
1.85-1.897.70.36419080.9550.1360.391.60699.8
1.89-1.937.80.2919100.9720.1070.311.67799.9
1.93-1.977.70.23619580.980.0870.2531.78599.9
1.97-2.027.80.18419010.9880.0680.1971.8999.7
2.02-2.077.70.16219040.990.060.1731.9799.7
2.07-2.147.70.1319450.9930.0480.1392.06599.7
2.14-2.27.70.11319370.9950.0420.122.17899.9
2.2-2.287.60.10119590.9940.0370.1082.314100
2.28-2.387.60.08919220.9950.0330.0952.31199.8
2.38-2.487.70.0819520.9960.030.0862.4199.5
2.48-2.617.60.07119440.9960.0270.0762.36299.7
2.61-2.787.60.06419400.9970.0240.0692.35799.8
2.78-2.997.60.05819990.9980.0220.0622.26499.8
2.99-3.297.60.05219620.9970.0190.0552.16699.8
3.29-3.777.70.04420120.9980.0160.0472.22599.9
3.77-4.757.50.04120300.9980.0150.0442.15399.8
4.75-507.10.03920240.9980.0160.0421.9792.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VI0

1vi0


Resolution: 1.755→27.689 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1915 4.97 %
Rwork0.2011 36648 -
obs0.2028 38563 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.01 Å2 / Biso mean: 38.6127 Å2 / Biso min: 16.71 Å2
Refinement stepCycle: final / Resolution: 1.755→27.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 49 271 3381
Biso mean--52.99 48.35 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213150
X-RAY DIFFRACTIONf_angle_d2.0184221
X-RAY DIFFRACTIONf_chiral_restr0.128479
X-RAY DIFFRACTIONf_plane_restr0.011531
X-RAY DIFFRACTIONf_dihedral_angle_d16.1081207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7554-1.79930.27951180.28532553267199
1.7993-1.8480.32441710.252525662737100
1.848-1.90230.28431360.245725902726100
1.9023-1.96370.27431010.237526242725100
1.9637-2.03390.291410.219725742715100
2.0339-2.11530.24341380.214125882726100
2.1153-2.21150.24431410.211125672708100
2.2115-2.32810.22381230.208226162739100
2.3281-2.47380.2431350.203726452780100
2.4738-2.66470.28061450.201125962741100
2.6647-2.93260.26441360.203726392775100
2.9326-3.35630.22091260.20926912817100
3.3563-4.22620.2211620.179926592821100
4.2262-27.69250.20161420.18882740288295

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