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- PDB-5zkm: Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7... -

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Basic information

Entry
Database: PDB / ID: 5zkm
TitleCrystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA TCTTCC
Components
  • DNA (5'-D(P*TP*CP*TP*TP*CP*C)-3')
  • SP_0782
KeywordsUNKNOWN FUNCTION/DNA / protein-DNA complex / UNKNOWN FUNCTION-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 TIGR4 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLu, G. / Li, S. / Zhu, J. / Yang, Y. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Key R&D Program of China2016YFA051201 China
the National Natural Sciences Foundation of China21575155 China
National Natural Sciences 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
DepositionMar 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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 1.3Nov 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

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Assembly

Deposited unit
A: SP_0782
B: DNA (5'-D(P*TP*CP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,3282
Polymers11,3282
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4690 Å2
Unit cell
Length a, b, c (Å)66.096, 66.096, 43.484
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 TIGR4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_0782 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2UPA7
#2: DNA chain DNA (5'-D(P*TP*CP*TP*TP*CP*C)-3')


Mass: 1735.167 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.: 80 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.8 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 11101 / % possible obs: 97.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.08 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Χ2: 0.954 / Net I/σ(I): 11 / Num. measured all: 73217
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.714.50.3489080.9380.1670.3880.84280.4
1.71-1.785.60.31310830.9660.1370.3430.84394.8
1.78-1.866.10.25410950.980.1090.2770.88898.6
1.86-1.966.70.19311500.990.080.2090.94199.7
1.96-2.087.10.13811340.9950.0560.1490.917100
2.08-2.247.30.11211410.9960.0450.120.966100
2.24-2.467.40.09111380.9970.0360.0970.975100
2.46-2.827.40.07611320.9970.030.0820.95299.9
2.82-3.556.90.06511480.9960.0270.071.185100
3.55-506.40.05111720.9960.0230.0570.92398.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OBH

3obh


Resolution: 1.65→33.048 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1026 10.05 %
Rwork0.1788 9183 -
obs0.1814 10209 89.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.42 Å2 / Biso mean: 16.9466 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: final / Resolution: 1.65→33.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms532 24 0 80 636
Biso mean---28.51 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005570
X-RAY DIFFRACTIONf_angle_d0.731773
X-RAY DIFFRACTIONf_chiral_restr0.05384
X-RAY DIFFRACTIONf_plane_restr0.00596
X-RAY DIFFRACTIONf_dihedral_angle_d22.02201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.7370.2376890.2092917100662
1.737-1.84590.23581110.18261152126378
1.8459-1.98840.21891350.18831315145090
1.9884-2.18840.1761880.16781382157098
2.1884-2.5050.19431850.176814371622100
2.505-3.15560.21681500.18514891639100
3.1556-33.05460.20411680.17331491165999

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