[English] 日本語
Yorodumi
- PDB-6jiq: Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more