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- PDB-5zqh: Crystal structure of Streptococcus transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 5zqh
TitleCrystal structure of Streptococcus transcriptional regulator
ComponentsPadR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Bacteria / PadR / antibiotic resistance / regulator / transcription
Function / homology
Function and homology information


Transcription 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
Similarity search - Domain/homology
PadR family transcriptional regulator / Transcriptional regulator, PadR family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKim, M. / Hong, M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015R1D1A1A01057574 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structure-based functional analysis of a PadR transcription factor from Streptococcus pneumoniae and characteristic features in the PadR subfamily-2.
Authors: Lee, C. / Kim, M.I. / Park, J. / Oh, H. / Kim, J. / Hong, J. / Jeon, B.Y. / Ka, H. / Hong, M.
History
DepositionApr 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.pdbx_descriptor
Revision 1.2Nov 22, 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_atoms
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: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)11,8791
Polymers11,8791
Non-polymers00
Water28816
1
A: PadR family transcriptional regulator

A: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)23,7572
Polymers23,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2690 Å2
ΔGint-22 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.301, 30.612, 51.481
Angle α, β, γ (deg.)90.000, 127.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PadR family transcriptional regulator / putative PadR-like protein


Mass: 11878.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229FJD3, UniProt: A5M9R0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.2M Ammonium sulfate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 4026 / % possible obs: 97.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.027 / Rrim(I) all: 0.047 / Χ2: 2.556 / Net I/σ(I): 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.10.0752000.9940.0510.0913.002100
2.44-2.4930.0632120.9950.0440.0772.999.5
2.49-2.533.10.0621800.9940.0430.0762.62798.9
2.53-2.5930.0582310.9920.0410.0712.87499.6
2.59-2.6430.0541820.9960.0370.0652.8399.5
2.64-2.72.90.0561990.990.040.0692.80698.5
2.7-2.7730.0542140.9950.0370.0662.81499.5
2.77-2.8530.0491890.9950.0340.062.69999
2.85-2.9330.0482040.9940.0340.0592.64699
2.93-3.0230.0451980.9960.0310.0552.597100
3.02-3.133.10.0452120.9950.030.0542.89699.1
3.13-3.262.90.0431980.9970.030.0522.75100
3.26-3.4130.0372200.9970.0260.0462.346100
3.41-3.5830.0371880.9960.0260.0452.38999.5
3.58-3.812.90.0372140.9950.0260.0462.28799.1
3.81-4.130.0351970.9960.0240.0422.4598.5
4.1-4.5230.0311990.9970.0210.0381.83895.2
4.52-5.172.80.0312040.9970.0220.0391.93996.2
5.17-6.512.90.032070.9970.0210.037298.6
6.51-502.70.0351780.9930.0250.0432.20978.1

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Processing

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

4esf


Resolution: 2.4→40.63 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.962 / ESU R Free: 0.344 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2982 203 5 %RANDOM
Rwork0.2909 ---
obs0.2912 3820 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 36.56 Å2 / Biso mean: 10.43 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-1.79 Å2
2--4.12 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.4→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 0 16 843
Biso mean---20.69 -
Num. residues----101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02838
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9731127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.235599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.97524.88443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.15615158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.513156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021633
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.419 19 -
Rwork0.3 288 -
obs--100 %

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