[English] 日本語
Yorodumi
- PDB-4yft: HUab-20bp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yft
TitleHUab-20bp
Components
  • (synthetic DNA strand) x 2
  • DNA-binding protein HU-alpha
  • DNA-binding protein HU-beta
KeywordsDNA BINDING PROTEIN/DNA / HU-DNA / transcription / pathogenicity / 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 (> 10) / : / DNA-binding protein HU-alpha / DNA-binding protein HU-alpha / DNA-binding protein HU-beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.914 Å
AuthorsHammel, M. / Reyes, F.E. / Parpana, R. / Tainer, J.A. / Adhya, S. / Amlanjyoti, D.
CitationJournal: Sci Adv / Year: 2016
Title: HU multimerization shift controls nucleoid compaction.
Authors: Hammel, M. / Amlanjyoti, D. / Reyes, F.E. / Chen, J.H. / Parpana, R. / Tang, H.Y. / Larabell, C.A. / Tainer, J.A. / Adhya, S.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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-beta
B: synthetic DNA strand
D: synthetic DNA strand
C: DNA-binding protein HU-alpha


Theoretical massNumber of molelcules
Total (without water)24,6214
Polymers24,6214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.036, 83.036, 63.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein DNA-binding protein HU-beta


Mass: 9169.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupB / Production host: Escherichia coli (E. coli) / References: UniProt: N4NVB4, UniProt: P0ACF4*PLUS
#2: DNA chain synthetic DNA strand


Mass: 2605.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain synthetic DNA strand


Mass: 3296.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Protein DNA-binding protein HU-alpha / HU-2 / NS2


Mass: 9549.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF2, UniProt: P0ACF0*PLUS
Sequence detailsDNA sample sequence used in experiment is 5'-GTTCAATTGTTGTTAACTTG-3'. But the asymmetric unit ...DNA sample sequence used in experiment is 5'-GTTCAATTGTTGTTAACTTG-3'. But the asymmetric unit contains multiple, out-of-register duplex positions, so the DNA chain is modeled according to averaged density.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 30% PEG MME 550, 0.05 M CaCl2

-
Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2013 / Details: Q315R
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.914→83.036 Å / Num. all: 5183 / Num. obs: 5183 / % possible obs: 99.9 % / Redundancy: 27.4 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 23.2 / Num. measured all: 141920
Reflection shellResolution: 2.914→2.924 Å / Redundancy: 29.2 % / Rmerge(I) obs: 2.187 / Mean I/σ(I) obs: 2.188 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
Aimlessdata scaling
BUSTER2.10.0refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUL

1mul


Resolution: 2.914→58.72 Å / Cor.coef. Fo:Fc: 0.9226 / Cor.coef. Fo:Fc free: 0.8968 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all ...Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all nucleotides, and the DNA chain was built accordingly.
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 240 4.65 %RANDOM
Rwork0.2146 ---
obs0.2162 5161 99.44 %-
Displacement parametersBiso max: 174.94 Å2 / Biso mean: 73.8327 Å2 / Biso min: 38.12 Å2
Baniso -1Baniso -2Baniso -3
1--5.2527 Å20 Å20 Å2
2---5.2527 Å20 Å2
3---10.5054 Å2
Refine analyzeLuzzati coordinate error obs: 0.391 Å
Refinement stepCycle: LAST / Resolution: 2.914→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 397 0 0 1447
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d471SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes173HARMONIC5
X-RAY DIFFRACTIONt_it1498HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion212SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1635SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1498HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2089HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion22.24
LS refinement shellResolution: 2.91→3.25 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.4048 68 4.84 %
Rwork0.2202 1336 -
all0.2283 1404 -
obs--99.44 %

+
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