[English] 日本語
Yorodumi
- PDB-4yf0: HU38-19bp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yf0
TitleHU38-19bp
Components
  • (synthetic DNA strand) x 2
  • DNA-binding protein HU-alpha
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 DNA 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 DNA 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 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 24, 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-alpha
B: DNA-binding protein HU-alpha
C: synthetic DNA strand
D: synthetic DNA strand


Theoretical massNumber of molelcules
Total (without water)26,2244
Polymers26,2244
Non-polymers00
Water00
1
A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha
C: synthetic DNA strand
D: synthetic DNA strand

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha
C: synthetic DNA strand
D: synthetic DNA strand

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha
C: synthetic DNA strand
D: synthetic DNA strand


Theoretical massNumber of molelcules
Total (without water)78,67212
Polymers78,67212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/61
Unit cell
Length a, b, c (Å)74.890, 74.890, 220.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

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


Mass: 9702.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupA, b4000, JW3964 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF2, UniProt: P0ACF0*PLUS
#2: DNA chain synthetic DNA strand


Mass: 3196.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain synthetic DNA strand


Mass: 3623.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
Sequence detailsDNA sample sequence used in experiment is 5'-TTCAATTGTTGTTAACTTG-3'. But the asymmetric unit ...DNA sample sequence used in experiment is 5'-TTCAATTGTTGTTAACTTG-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: 3.66 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis-Tris pH 5.8, 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: 2.79→110.103 Å / Num. all: 9847 / Num. obs: 9847 / % possible obs: 100 % / Redundancy: 39.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 35.1 / Num. measured all: 386391
Reflection shellResolution: 2.79→2.8 Å / Redundancy: 31.76 % / Rmerge(I) obs: 1.913 / Mean I/σ(I) obs: 2.199 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

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

1mul


Resolution: 2.79→64.86 Å / Cor.coef. Fo:Fc: 0.9117 / Cor.coef. Fo:Fc free: 0.9008 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.502 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.575 / SU Rfree Blow DPI: 0.312 / SU Rfree Cruickshank DPI: 0.303
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
Rfree0.2649 469 4.79 %RANDOM
Rwork0.2472 ---
obs0.2481 9783 99.95 %-
Displacement parametersBiso max: 222.92 Å2 / Biso mean: 101.8625 Å2 / Biso min: 49.28 Å2
Baniso -1Baniso -2Baniso -3
1-5.0766 Å20 Å20 Å2
2--5.0766 Å20 Å2
3----10.1533 Å2
Refine analyzeLuzzati coordinate error obs: 0.664 Å
Refinement stepCycle: LAST / Resolution: 2.79→64.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 455 0 0 1670
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d555SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes197HARMONIC5
X-RAY DIFFRACTIONt_it1724HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion243SEMIHARMONIC5
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_contact1761SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1724HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2406HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion21.67
LS refinement shellResolution: 2.79→3.12 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2758 138 5.13 %
Rwork0.2702 2550 -
all0.2705 2688 -
obs--99.95 %
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)
14.8828-1.31441.72342.36011.29168.9290.44050.0656-0.3926-0.28850.2953-0.0590.95130.5292-0.73580.00180.2558-0.2402-0.1027-0.1920.049611.4421-16.586120.1607
22.774-0.5452-0.01553.3728-0.52221.81060.2221-0.07860.0758-0.3140.0579-0.0250.07330.6219-0.2801-0.10030.1724-0.1372-0.0524-0.1529-0.112116.2586-13.694122.9912
35.8835-2.2391.7278-0.10693.897516.6309-0.22760.65120.4607-0.1054-0.4692-0.3408-0.1828-0.0450.69680.49720.0824-0.0916-0.2357-0.4039-0.296431.9253-24.97913.2763
410.37850.911-7.44694.31452.42187.9258-0.1221-0.45520.07040.23910.46930.37830.5375-0.3025-0.3473-0.13590.1232-0.1397-0.13460.024-0.0654-6.1481-9.270136.7483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 90
2X-RAY DIFFRACTION2{ B|* }B0 - 90
3X-RAY DIFFRACTION3{ C|* }C1 - 11
4X-RAY DIFFRACTION4{ D|* }D1 - 12

+
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