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- PDB-6abq: Crystal structure of transcription factor from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 6abq
TitleCrystal structure of transcription factor from Listeria monocytogenes
ComponentsPadR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Bacteria / PadR / transcription factor
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / PadR family transcriptional regulator
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLee, C. / Hong, M.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2018R1A2B6001619 Korea, Republic Of
National Research Foundation (Korea)2015R1D1A1A0105757 Korea, Republic Of
CitationJournal: Plos One / Year: 2019
Title: Structure-based molecular characterization and regulatory mechanism of the LftR transcription factor from Listeria monocytogenes: Conformational flexibilities and a ligand-induced regulatory mechanism.
Authors: Lee, C. / Kim, M.I. / Park, J. / Hong, M.
History
DepositionJul 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: 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

Downloads & links

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Assembly

Deposited unit
B: PadR family transcriptional regulator
A: PadR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9094
Polymers25,8382
Non-polymers712
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-45 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.955, 73.955, 66.313
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 PadR family transcriptional regulator


Mass: 12918.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: C7K50_07245, CDR86_13565, LmNIHS28_00834 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L8DXR9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M lithium chloride, 0.1 M citric acid, pH 5.5, and 30% polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.0003 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.3→64 Å / Num. obs: 9616 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Χ2: 1.81 / Net I/σ(I): 22.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.347.30.0754580.9950.030.0812.038100
2.34-2.387.20.0714820.9960.0280.0772.078100
2.38-2.437.30.0694640.9960.0270.0741.936100
2.43-2.487.20.0644770.9960.0250.0681.894100
2.48-2.537.30.0634730.9980.0250.0681.861100
2.53-2.597.20.0634640.9970.0250.0681.889100
2.59-2.667.20.0594990.9980.0230.0641.91100
2.66-2.737.20.0564610.9980.0220.061.858100
2.73-2.817.30.0544660.9980.0210.0581.802100
2.81-2.97.20.0524820.9980.0210.0561.826100
2.9-37.20.054920.9980.020.0541.77100
3-3.127.20.0474620.9980.0190.0511.868100
3.12-3.267.20.0434790.9990.0170.0471.678100
3.26-3.447.10.0424920.9980.0170.0451.747100
3.44-3.657.10.0394740.9980.0160.0421.696100
3.65-3.937.10.0374910.9990.0150.041.612100
3.93-4.3370.0374920.9980.0150.041.705100
4.33-4.956.90.0364910.9990.0150.0391.561100
4.95-6.246.80.0385080.9980.0160.0411.553100
6.24-505.80.0415090.9970.0190.0461.93295

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ESF

4esf


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.542 / ESU R Free: 0.271 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 486 5.1 %RANDOM
Rwork0.2048 ---
obs0.2072 9111 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.13 Å2 / Biso mean: 25.591 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 2 129 1873
Biso mean--13.43 10.38 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021811
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0022434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0635225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78724.41677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1215368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.891510
X-RAY DIFFRACTIONr_chiral_restr0.090.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211318
LS refinement shellResolution: 2.301→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 34 -
Rwork0.205 659 -
all-693 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.48683.32571.53822.50950.71711.3982-0.21160.06140.55820.1178-0.0310.3050.1090.01370.24250.2238-0.04330.00270.1716-0.01370.125424.02995.910.959
24.3186-0.2529-0.1341.54230.15722.621-0.19250.2543-0.0551-0.11710.1360.11650.0588-0.12340.05640.0694-0.0255-0.01080.03830.00340.012836.427105.356-4.903
31.7934-0.84360.26782.2494-0.6791.007-0.08480.05490.00970.04540.0069-0.0697-0.0148-0.05660.0780.0724-0.0158-0.00350.0762-0.01420.00841.221108.8381.437
45.92846.3853-1.406110.3952-1.16331.090.07730.1403-0.44630.10290.0358-0.3851-0.13830.0076-0.11310.11940.020.03530.0638-0.01390.114141.23988.173-2.49
57.99622.14692.65353.4168-3.06125.9428-0.12350.1954-0.0938-0.25240.11870.00220.1868-0.05650.00470.16790.0276-0.03360.0681-0.04580.167127.33877.877-2.004
64.6625-5.519-4.25226.79714.24716.51190.0315-0.00180.02870.0459-0.1332-0.0908-0.36610.26210.10170.1117-0.0094-0.02690.14610.02770.10736.93687.5837.505
76.2164-1.0507-0.56453.9233-1.00293.7651-0.16970.0087-0.263-0.09990.0466-0.39710.19910.29170.12310.05480.01560.0220.0316-0.00840.063526.28975.259.998
89.3558-1.46230.27051.7917-0.47741.01220.1124-0.46380.118-0.0315-0.0594-0.28320.06320.2645-0.05290.1153-0.0359-0.01610.1199-0.01420.067329.74580.87614.968
91.24130.37760.14024.4719-3.6244.7196-0.0012-0.0753-0.1223-0.0248-0.0452-0.04490.24550.06430.04640.0470.00740.00160.0289-0.01730.047817.7776.40714.299
1010.49033.6162-8.62961.3286-3.24438.255-0.17470.2239-0.4688-0.07380.033-0.10950.0863-0.14460.14160.11970.01890.00780.0767-0.00550.08128.73891.987-7.544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 13
2X-RAY DIFFRACTION2A14 - 38
3X-RAY DIFFRACTION3A39 - 81
4X-RAY DIFFRACTION4A82 - 99
5X-RAY DIFFRACTION5A100 - 105
6X-RAY DIFFRACTION6B3 - 9
7X-RAY DIFFRACTION7B10 - 36
8X-RAY DIFFRACTION8B37 - 56
9X-RAY DIFFRACTION9B57 - 90
10X-RAY DIFFRACTION10B91 - 108

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