[English] 日本語
Yorodumi
- PDB-6qlc: The ssDNA-binding RNA polymerase cofactor Drc from Pseudomonas ph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qlc
TitleThe ssDNA-binding RNA polymerase cofactor Drc from Pseudomonas phage LUZ7
ComponentsssDNA binding RNA Polymerase cofactor
KeywordsVIRAL PROTEIN / ssDNA binding
Function / homologyPHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas phage LUZ7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsDe Zitter, E. / Boon, M. / De Smet, J. / Lavigne, R. / Van Meervelt, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
KU LeuvenGOA-project KUL_3E140356 Belgium
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses.
Authors: Boon, M. / De Zitter, E. / De Smet, J. / Wagemans, J. / Voet, M. / Pennemann, F.L. / Schalck, T. / Kuznedelov, K. / Severinov, K. / Van Meervelt, L. / De Maeyer, M. / Lavigne, R.
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 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 / _citation_author.name
Revision 1.2Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ssDNA binding RNA Polymerase cofactor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6562
Polymers11,5611
Non-polymers951
Water54030
1
A: ssDNA binding RNA Polymerase cofactor
hetero molecules

A: ssDNA binding RNA Polymerase cofactor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3124
Polymers23,1222
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,-y-1/2,-z-3/41
Buried area4280 Å2
ΔGint-38 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.826, 88.826, 63.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein ssDNA binding RNA Polymerase cofactor / ssDNA-binding RNA polymerase cofactor Drc


Mass: 11561.232 Da / Num. of mol.: 1 / Fragment: ssDNA binding protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage LUZ7 (virus) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: C8ZKB3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.8 M ammonium phosphate monobasic 0.1 M sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000, 2.07333
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.073331
ReflectionResolution: 2.2→44.42 Å / Num. obs: 6690 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 48.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.013 / Rrim(I) all: 0.047 / Net I/σ(I): 31.3 / Num. measured all: 86244
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.2713.70.4535710.9680.1260.471100
9.07-44.4210.50.0281190.9990.010.0399

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
XDSOct 2015data reduction
Aimless0.5.25data scaling
SHELX2013/2phasing
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.2→44.413 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36.1
RfactorNum. reflection% reflection
Rfree0.2859 354 5.3 %
Rwork0.2272 --
obs0.2302 6673 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.55 Å2 / Biso mean: 58.1697 Å2 / Biso min: 33.76 Å2
Refinement stepCycle: final / Resolution: 2.2→44.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms650 0 5 30 685
Biso mean--70.08 64.6 -
Num. residues----81
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007680
X-RAY DIFFRACTIONf_angle_d0.882917
X-RAY DIFFRACTIONf_chiral_restr0.047103
X-RAY DIFFRACTIONf_plane_restr0.005119
X-RAY DIFFRACTIONf_dihedral_angle_d8.039582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.51840.38441240.27220452169
2.5184-3.17280.33091280.305220712199
3.1728-44.4220.25271020.197722032305

+
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://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