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

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Basic information

Entry
Database: PDB / ID: 6abt
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: 2.8 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


Theoretical massNumber of molelcules
Total (without water)22,6922
Polymers22,6922
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.024, 67.024, 90.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein PadR family transcriptional regulator


Mass: 11346.174 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: with 0.2 M calcium acetate, 0.1 M cacodylate acid, pH 6.3, and 48 % polyethylene glycol 600

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.0003 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.8→58.04 Å / Num. obs: 5721 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Χ2: 2.382 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.857.30.3342660.990.1330.361.635100
2.85-2.97.50.2873020.9920.1150.311.683100
2.9-2.967.30.3462730.9880.1390.3731.784100
2.96-3.027.40.2782970.9880.1110.2991.866100
3.02-3.087.40.2252660.9910.090.2431.724100
3.08-3.157.50.2422950.9880.0970.2611.852100
3.15-3.237.40.1842850.9910.0730.1981.988100
3.23-3.327.40.1452900.9970.0580.1571.968100
3.32-3.427.40.1342860.9960.0540.1452.114100
3.42-3.537.40.1322850.9960.0520.1422.312100
3.53-3.657.40.1072760.9960.0430.1162.425100
3.65-3.87.40.0992780.9970.040.1072.744100
3.8-3.977.30.0812990.9980.0330.0882.653100
3.97-4.187.30.0732870.9980.0290.0792.817100
4.18-4.447.20.0652900.9980.0270.0713.226100
4.44-4.797.30.0582880.9980.0240.0632.841100
4.79-5.277.20.0592800.9990.0240.0642.909100
5.27-6.037.10.0652960.9980.0260.072.944100
6.03-7.5970.0592870.9970.0240.0633.031100
7.59-506.10.0512950.9950.0220.0563.33897.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ABQ

6abq


Resolution: 2.8→58.04 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.911 / SU B: 42 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 295 5.2 %RANDOM
Rwork0.2553 ---
obs0.2573 5406 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.4 Å2 / Biso mean: 70 Å2 / Biso min: 55.74 Å2
Baniso -1Baniso -2Baniso -3
1-6.23 Å23.11 Å20 Å2
2--6.23 Å2-0 Å2
3----20.21 Å2
Refinement stepCycle: final / Resolution: 2.8→58.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 0 4 1527
Biso mean---67.75 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021556
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9862099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20124.09861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.35415279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.076157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211139
LS refinement shellResolution: 2.801→2.874 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 21 -
Rwork0.221 398 -
all-419 -
obs--99.05 %
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)
19.4428-0.365-7.131711.8835-19.892439.68510.3884-0.94550.62640.25620.74470.3713-0.7778-0.3481-1.13310.5454-0.0922-0.0630.8575-0.20140.9676-4.31-17.4720.7
24.63232.77734.04093.78495.03099.1144-0.08330.7181-0.61620.6301-0.1614-0.06851.2206-0.40830.24480.3388-0.23020.16120.3777-0.08570.99641.296-27.358.309
35.5111.1282-1.06785.02661.43596.4562-0.32130.15670.1808-0.38480.4537-0.1337-1.1574-0.1797-0.13240.333-0.02620.04720.2884-0.02020.85923.3-18.48612.633
49.0509-0.47264.4773.06550.29673.558-0.4175-0.1998-0.0546-0.31710.12510.0816-0.5951-0.07390.29250.17430.02560.05630.14240.06990.7999-4.618-22.24913.567
511.41363.55463.6552.80610.752255.8744-0.18110.39970.3812-0.1617-0.27430.099-0.6297-1.98350.45550.24250.08870.03560.25270.11050.9143-20.497-22.45-5.944
623.6734-10.03021.839130.631934.91848.44580.30520.56580.9996-0.12390.0395-0.7392-0.00110.4414-0.34470.808-0.15430.03980.70390.02861.1028-12.982-12.93-11.069
77.7439-5.4957-5.5016.25374.6545.8024-0.17140.7277-0.26121.3227-0.51580.28210.8456-1.24340.68710.7356-0.11490.12540.4763-0.06571.1197-24.318-12.409-18.806
84.23260.2429-4.37411.3366-8.097420.9903-0.52270.00540.01690.64820.3471-0.23330.09920.86880.17560.54060.15450.1020.1734-0.06310.8931-21.161-6.358-12.025
940.9707-5.8372-25.83481.11462.115725.02-0.11940.2616-0.03810.0774-0.1927-0.0907-0.19370.72110.3120.5721-0.2118-0.12880.1777-0.07930.8646-11.485-7.338-23.819
104.1186-3.80192.74536.4553-5.47647.6078-0.0311-0.156-0.0162-0.0193-0.1364-0.19150.1640.2330.16760.00780.0102-0.00960.0505-0.09270.7692-15.893-17.082-20.025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 14
2X-RAY DIFFRACTION2A15 - 38
3X-RAY DIFFRACTION3A39 - 67
4X-RAY DIFFRACTION4A68 - 93
5X-RAY DIFFRACTION5A94 - 104
6X-RAY DIFFRACTION6B7 - 14
7X-RAY DIFFRACTION7B15 - 35
8X-RAY DIFFRACTION8B36 - 49
9X-RAY DIFFRACTION9B50 - 57
10X-RAY DIFFRACTION10B58 - 104

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