[English] 日本語
Yorodumi
- PDB-6o6k: HUaa 19bp SYM DNA pH 5.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o6k
TitleHUaa 19bp SYM DNA pH 5.5
Components
  • DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3')
  • DNA (5'-D(P*CP*AP*TP*CP*AP*TP*GP*AP*AP*A)-3')
  • DNA-binding protein HU-alpha
Keywordsdna binding protein/dna / Nucleoid Associated Protein / DNA supercoiling / Histone like proteins / DNA BINDING PROTEIN / dna binding protein-dna complex
Function / homology
Function and homology information


HU-DNA complex / DnaA-HU complex / bacterial nucleoid packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding ...HU-DNA complex / DnaA-HU complex / bacterial nucleoid packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding / identical protein binding / membrane / cytosol
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA-binding protein HU-alpha / DNA-binding protein HU-alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.601 Å
AuthorsRemesh, S.G. / Hammel, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)Integrated Diffraction Analysis Technologies United States
CitationJournal: Nat Commun / Year: 2020
Title: Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.
Authors: Remesh, S.G. / Verma, S.C. / Chen, J.H. / Ekman, A.A. / Larabell, C.A. / Adhya, S. / Hammel, M.
History
DepositionMar 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha
C: DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3')
D: DNA (5'-D(P*CP*AP*TP*CP*AP*TP*GP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)25,1714
Polymers25,1714
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-48 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.790, 84.790, 63.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein DNA-binding protein HU-alpha / HU-2 / NS2


Mass: 9549.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hupA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0ACF2, UniProt: P0ACF0*PLUS
#2: DNA chain DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3')


Mass: 3034.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*CP*AP*TP*CP*AP*TP*GP*AP*AP*A)-3')


Mass: 3037.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.02M ZnCl2, 20% PEG 3350 / PH range: 5-6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.994→84.789 Å / Num. all: 71317 / Num. obs: 2939 / % possible obs: 99.7 % / Redundancy: 13.8 % / CC1/2: 1 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.141 / Net I/σ(I): 15.1
Reflection shellResolution: 3.602→3.73 Å / Redundancy: 12.9 % / Num. unique obs: 18426 / CC1/2: 0.245 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YEX and DNA

4yex


Resolution: 3.601→59.956 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.74
RfactorNum. reflection% reflection
Rfree0.3019 294 10.01 %
Rwork0.2523 --
obs0.2571 2937 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.601→59.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 409 0 0 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031544
X-RAY DIFFRACTIONf_angle_d0.5252158
X-RAY DIFFRACTIONf_dihedral_angle_d25.279592
X-RAY DIFFRACTIONf_chiral_restr0.034262
X-RAY DIFFRACTIONf_plane_restr0.002203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6007-4.53620.38111420.28741279X-RAY DIFFRACTION100
4.5362-59.96390.26771520.23761365X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2949-0.192-0.02920.0119-0.17020.04711.00910.09110.09062.3441-0.44031.03640.5492-0.142601.0895-0.2490.2860.73250.03680.6975-6.660516.6635.33
20.9354-0.3580.8265-0.0521-0.41-0.04741.6490.37096.03520.8854-1.7714-2.25840.0059-1.1273-00.26660.19320.02611.02960.24251.48641.85228.016526.5261
30.04570.0264-0.0424-0.14240.0480.008-0.94360.20680.5359-0.6501-1.8635-2.5846-0.32960.021-01.44750.5705-0.07012.05250.53841.71485.596830.41631.5591
40.13430.0194-0.04280.04880.24870.22490.13341.5462-1.038-1.6748-0.07881.49790.6065-0.468200.71240.16680.00171.36320.35450.86858.526915.627120.0921
5-0.0153-0.0561-0.1771-0.04730.0175-0.1027-0.45980.53941.4613-0.1008-2.34230.4821-1.11022.043901.0218-0.05450.0791.5426-0.44322.15064.229431.275535.5019
60.60520.3623-0.67060.4133-0.65490.2762-0.4261-0.271-0.10040.504-0.25840.64690.9385-0.445800.6269-0.0778-0.05550.6334-0.01680.60420.529916.593930.9966
7-0.4206-0.0060.50640.04790.1178-0.2133-1.98093.7257-0.3922-0.54881.15363.83130.5675-0.4837-00.6006-0.2115-0.28351.32370.45010.5926-1.874420.589417.0265
80.2330.01210.87590.0252-0.29060.27410.87480.39520.2033-0.338-0.31110.3155-0.28640.2457-01.4921-0.0693-0.21191.52750.2471.4811-21.034722.914817.7641
9-0.5571-0.02720.21720.03020.4226-0.00910.5155-0.1020.25870.29780.0744-0.5728-0.3633-1.453701.0728-0.11110.05721.33730.2371.0022-19.953522.020314.6198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:17 )A1 - 17
2X-RAY DIFFRACTION2( CHAIN A AND RESID 18:53 )A18 - 53
3X-RAY DIFFRACTION3( CHAIN A AND RESID 54:75 )A54 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:90 )A76 - 90
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:17 )B1 - 17
6X-RAY DIFFRACTION6( CHAIN B AND RESID 18:44 )B18 - 44
7X-RAY DIFFRACTION7( CHAIN B AND RESID 45:89 )B45 - 89
8X-RAY DIFFRACTION8( CHAIN C AND RESID 5:10 )C5 - 10
9X-RAY DIFFRACTION9( CHAIN D AND RESID 1:10 )D1 - 10

+
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