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

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Basic information

Entry
Database: PDB / ID: 5gpa
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 ...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
Transcriptional regulator (TetR/AcrR family)
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsLee, J.Y. / Yeo, H.K. / Park, Y.W.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Research Foundation of KoreaNRF; 2014R1A1A1A05008017 Korea, Republic Of
Research CenterARC; 710003-03 Korea, Republic Of
Global PhD Fellowship programD_1300001227 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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: Transcriptional regulator (TetR/AcrR family)
B: Transcriptional regulator (TetR/AcrR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7684
Polymers44,6522
Non-polymers1162
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-33 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.393, 56.393, 199.607
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 22325.998 Da / Num. of mol.: 2 / Mutation: R117A
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
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: 2.05→50 Å / Num. obs: 24026 / % possible obs: 99.6 % / Redundancy: 10.4 % / Biso Wilson estimate: 36.16 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Χ2: 2.094 / Net I/σ(I): 13.8 / Num. measured all: 249225
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.0910.70.52111960.9490.1660.5481.699100
2.09-2.1210.60.39911630.9730.1280.421.763100
2.12-2.1610.80.35512070.9790.1130.3731.778100
2.16-2.2110.70.30811360.9780.0980.3241.832100
2.21-2.2610.70.27812110.9830.0890.2921.832100
2.26-2.3110.70.22911520.990.0730.2411.866100
2.31-2.3710.70.20912050.9890.0670.221.957100
2.37-2.4310.70.18311760.9920.0590.1931.94100
2.43-2.510.70.15911690.9930.0510.1671.927100
2.5-2.5810.60.13412130.9950.0430.1411.935100
2.58-2.6810.70.12511880.9960.040.1312.003100
2.68-2.7810.60.09511910.9980.030.11.964100
2.78-2.9110.60.08611940.9980.0280.092.069100
2.91-3.0610.50.07712010.9980.0250.0812.127100
3.06-3.2510.50.06612100.9980.0210.072.289100
3.25-3.5110.30.05512350.9990.0180.0582.471100
3.51-3.8610.10.04611980.9990.0150.0492.557100
3.86-4.429.90.04412510.9990.0150.0462.69599.9
4.42-5.569.60.04112610.9990.0140.0442.60999.6
5.56-508.10.04512690.9980.0170.0482.77792.8

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Processing

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

5gp9


Resolution: 2.051→19.685 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1198 5.01 %RANDOM
Rwork0.2037 22735 --
obs0.2066 23933 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.95 Å2 / Biso mean: 43.1658 Å2 / Biso min: 18.63 Å2
Refinement stepCycle: final / Resolution: 2.051→19.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 0 91 3077
Biso mean---45.55 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093043
X-RAY DIFFRACTIONf_angle_d1.1174097
X-RAY DIFFRACTIONf_chiral_restr0.046473
X-RAY DIFFRACTIONf_plane_restr0.005519
X-RAY DIFFRACTIONf_dihedral_angle_d16.0221136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0508-2.13280.31661420.234124762618100
2.1328-2.22970.26791300.225524852615100
2.2297-2.34710.2831120.221625232635100
2.3471-2.49390.3071280.220224742602100
2.4939-2.6860.27861500.224125022652100
2.686-2.95550.28331360.216525162652100
2.9555-3.38130.27881230.214125322655100
3.3813-4.2530.2461310.184425882719100
4.253-19.68610.23261460.19172639278597

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