[English] 日本語
Yorodumi
- PDB-5k5o: Structure of AspA-26mer DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k5o
TitleStructure of AspA-26mer DNA complex
Components
  • (DNA (26-MER)) x 2
  • AspA
KeywordsTRANSCRIPTION/DNA / AspA / centromere DNA / DNA segregation / pNOB8 / archaea / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / identical protein binding
Similarity search - Function
Winged helix DNA-binding domain / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / 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 ...Winged helix DNA-binding domain / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / 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
DNA / DNA (> 10) / HTH arsR-type domain-containing protein
Similarity search - Component
Biological speciesSulfolobus sp. NOB8H2 (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsSchumacher, M.
CitationJournal: Science / Year: 2015
Title: Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.
Authors: Schumacher, M.A. / Tonthat, N.K. / Lee, J. / Rodriguez-Castaneda, F.A. / Chinnam, N.B. / Kalliomaa-Sanford, A.K. / Ng, I.W. / Barge, M.T. / Shaw, P.L. / Barilla, D.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AspA
B: AspA
C: AspA
D: AspA
N: DNA (26-MER)
M: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)61,6756
Polymers61,6756
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-96 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.627, 96.627, 187.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein
AspA


Mass: 11425.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus sp. NOB8H2 (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: O93706
#2: DNA chain DNA (26-MER)


Mass: 7987.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 7987.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 71.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M citrate, 0.1 M cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.18
ReflectionResolution: 3.2→50.005 Å / Num. obs: 14191 / % possible obs: 84.58 % / Redundancy: 2 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.5
Reflection shellResolution: 3.2→3.32 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RS8

4rs8


Resolution: 3.2→50.005 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.42 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2894 1584 11.16 %
Rwork0.2569 --
obs0.2602 14191 84.58 %
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.939 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2728 Å20 Å20 Å2
2---8.2728 Å2-0 Å2
3---16.5456 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 1060 0 0 3999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014170
X-RAY DIFFRACTIONf_angle_d1.4735851
X-RAY DIFFRACTIONf_dihedral_angle_d25.2431658
X-RAY DIFFRACTIONf_chiral_restr0.068681
X-RAY DIFFRACTIONf_plane_restr0.008542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2036-3.3180.5186740.4667694X-RAY DIFFRACTION42
3.318-3.45080.5811860.3955836X-RAY DIFFRACTION50
3.4508-3.60780.4071160.34551035X-RAY DIFFRACTION64
3.6078-3.79790.33231460.30151318X-RAY DIFFRACTION79
3.7979-4.03560.29431530.27861379X-RAY DIFFRACTION82
4.0356-4.34690.28161590.24721440X-RAY DIFFRACTION86
4.3469-4.78370.30181660.24351494X-RAY DIFFRACTION89
4.7837-5.47460.29081680.24761493X-RAY DIFFRACTION89
5.4746-6.8920.26851700.24441522X-RAY DIFFRACTION90
6.892-40.83160.22131710.20641553X-RAY DIFFRACTION89

+
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