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- PDB-7wjp: Structure of PadR-like protein from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 7wjp
TitleStructure of PadR-like protein from Listeria monocytogenes
ComponentsPadR family transcriptional regulator
KeywordsTRANSCRIPTION / listeria monocytogenes / Transcription factor / regulation / PadR
Function / homology: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / PadR family transcriptional regulator
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHong, M. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1F1A1045940 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structure-based molecular characterization of the LltR transcription factor from Listeria monocytogenes.
Authors: Kim, J. / Park, J. / Choi, Z. / Hong, M.
History
DepositionJan 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)12,7141
Polymers12,7141
Non-polymers00
Water30617
1
A: PadR family transcriptional regulator

A: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)25,4292
Polymers25,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2990 Å2
ΔGint-31 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.182, 72.182, 46.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-212-

HOH

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Components

#1: Protein PadR family transcriptional regulator / Transcriptional regulator / PadR family


Mass: 12714.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D2INR9
#2: 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 M lithium chloride, 0.1 M MES, pH 6.5, 17% polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 6256 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 49.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 56.6
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.25 / Num. unique obs: 188 / CC1/2: 0.983 / CC star: 0.997 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQH

5zqh


Resolution: 2.25→36.09 Å / SU ML: 0.1646 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.9989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 318 5.11 %318
Rwork0.2249 5901 --
obs0.2282 6224 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.07 Å2
Refinement stepCycle: LAST / Resolution: 2.25→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 0 17 818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071816
X-RAY DIFFRACTIONf_angle_d0.93741099
X-RAY DIFFRACTIONf_chiral_restr0.0457123
X-RAY DIFFRACTIONf_plane_restr0.004134
X-RAY DIFFRACTIONf_dihedral_angle_d19.6086492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.830.35211500.27372881X-RAY DIFFRACTION99.9
2.83-36.090.27361680.21353020X-RAY DIFFRACTION99.78
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)
14.32680251340.58162478071-0.3504636295013.223528625582.714263947567.42784199344-0.07634102415890.25855340692-0.1741817031-0.318870321220.1838857608820.418448308582-0.35442868847-1.06295629823-0.01016485639360.255010956820.0558350059043-0.04516377751690.4243335016160.1168537361220.6243314522270.11249871607213.53836516929.71537968275
23.5208967479-0.168895681235-0.358936420656.036129447662.216836120255.915035229540.2103186714940.4204438853320.499733601041-0.527758859462-0.08408429735190.103630766924-0.570704488537-0.318685913518-0.1011576851260.3755972299650.0465093966953-0.005082472990290.3634144621840.05894311973090.4605971233172.0272093599621.88119248416.28943270755
39.236314122823.43455588634-1.660088062149.42116551939-2.1372047828.49694441795-0.1291864230351.71655916641.64983715374-0.7412060715280.842146979486-0.129805408311-1.332326557380.0219604958984-0.5810055819850.567422550991-0.00560070254570.01672215426290.4519077972040.1997126225761.004195975027.959382181830.21062566135.90922349249
47.287583608164.392394946373.030817778943.729573828881.141321654492.35076588330.27418041774-0.749803170708-0.7070443994161.55705781188-0.3616562797-0.3628430039010.100017669684-0.4135249225760.1271639215180.518100083365-0.07575474630220.09507945344840.414840679080.03508254610730.321345067446-0.147568974415.3037522043418.4443118269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 105 )

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