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- PDB-6jiq: Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7... -

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Basic information

Entry
Database: PDB / ID: 6jiq
TitleCrystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA dT6
Components
  • DNA (5'-D(*TP*TP*TP*TP*T)-3')
  • SP_0782
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional Co-activator pc4; Chain A - #70 / PC4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsFang, X. / Lu, G. / Li, S. / Zhu, J. / Yang, Y. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA051201 China
National Natural Science Foundation of China21575155 China
National Natural Science Foundation of China31370198 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins.
Authors: Li, S. / Lu, G. / Fang, X. / Ramelot, T.A. / Kennedy, M.A. / Zhou, X. / Gong, P. / Zhang, X. / Liu, M. / Zhu, J. / Yang, Y.
History
DepositionFeb 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 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
A: SP_0782
B: DNA (5'-D(*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)11,3732
Polymers11,3732
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.563, 66.563, 42.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein SP_0782


Mass: 9592.798 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: spr0690, sp_0782 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DQG2
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*T)-3')


Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.05 Å3/Da / Density % sol: 39.94 % / Mosaicity: 0.386 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 3.4 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 10786 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.14 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Χ2: 0.568 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.67-1.735.40.46710410.9410.2130.5150.44296
1.73-1.85.90.35910520.9670.160.3940.43498.9
1.8-1.886.40.26810750.9820.1150.2920.44100
1.88-1.986.30.17210730.9910.0750.1880.4799.9
1.98-2.16.50.11810750.9960.0490.1280.47799.4
2.1-2.2770.09110840.9970.0370.0980.513100
2.27-2.496.90.07410890.9970.0310.080.533100
2.49-2.866.30.05510820.9970.0240.060.56999.8
2.86-3.66.90.04510940.9980.0190.0490.77599.9
3.6-506.50.0411210.9980.0170.0430.94499.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OBH

3obh


Resolution: 1.67→33.282 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 31.11
RfactorNum. reflection% reflection
Rfree0.213 555 5.18 %
Rwork0.1996 --
obs0.2003 10716 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.01 Å2 / Biso mean: 34.4293 Å2 / Biso min: 20.88 Å2
Refinement stepCycle: final / Resolution: 1.67→33.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 64 0 41 639
Biso mean---39.29 -
Num. residues----71
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006616
X-RAY DIFFRACTIONf_angle_d0.82843
X-RAY DIFFRACTIONf_chiral_restr0.05192
X-RAY DIFFRACTIONf_plane_restr0.00698
X-RAY DIFFRACTIONf_dihedral_angle_d13.335349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6701-1.83820.29131310.26382500263198
1.8382-2.10420.23971250.20925362661100
2.1042-2.65090.2251570.218625182675100
2.6509-33.28810.19531420.185126072749100

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