[English] 日本語
Yorodumi
- PDB-7jy2: Z-DNA joint X-ray/Neutron -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jy2
TitleZ-DNA joint X-ray/Neutron
ComponentsChains: A,B
KeywordsDNA / Z-DNA / joint X-ray/Neutron / hydration / cryo neutron crystallography
Function / homologyDEUTERATED WATER / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHarp, J.M. / Coates, L. / Egli, M.
Citation
Journal: Nucleic Acids Res. / Year: 2021
Title: Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography.
Authors: Harp, J.M. / Coates, L. / Sullivan, B. / Egli, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Joint X-ray and neutron refinement with phenix.refine.
Authors: Afonine, P.V. / Mustyakimov, M. / Grosse-Kunstleve, R.W. / Moriarty, N.W. / Langan, P. / Adams, P.D.
History
DepositionAug 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chains: A,B
B: Chains: A,B


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-2 kcal/mol
Surface area5570 Å2
Unit cell
Length a, b, c (Å)17.960, 31.150, 44.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: DNA chain Chains: A,B


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestN

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

-
Sample preparation

CrystalDensity Matthews: 1.7 Å3/Da / Density % sol: 27.69 % / Description: hexagonal plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.5 M (ND4)2SO4, 10 mM magnesium acetate, 50 mM perdeuterated 2-(N-morpholino)ethanesulfonic acid (MES)

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEORNL Spallation Neutron Source MANDI12.0-6.0
LIQUID ANODEExcillum MetalJet D2+ 70 kV21.3418
Detector
TypeIDDetectorDate
ORNL ANGER CAMERA1AREA DETECTOROct 24, 2018
Bruker PHOTON II2PIXELApr 4, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
121
261
31.34181
Reflection

Entry-ID: 7JY2

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Diffraction-IDNet I/σ(I)
1.5-14.67358784.25.895.530.918113.8
1-181833495.910.53.040.999212.8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
1.5-1.553.853070.482178.52
1-1.087.824070.985288.6

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SAINTdata reduction
Aimlessdata scaling
PHENIXphasing
Refinement

SU ML: 0.0589 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.2706 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 3qba

3qba

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)Diffraction-IDBiso mean (Å2)Rfactor obsNum. reflection Rfree% reflection Rfree (%)
1.5-14.67NEUTRON DIFFRACTION0.3030.27721930358584.021
1-18X-RAY DIFFRACTION0.1850.15631830795.9225.370.1593250710.26
Refinement stepCycle: LAST / Resolution: 1.5→14.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 77 317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116573
X-RAY DIFFRACTIONf_angle_d1.4385863
X-RAY DIFFRACTIONf_chiral_restr0.076847
X-RAY DIFFRACTIONf_plane_restr0.011846
X-RAY DIFFRACTIONf_dihedral_angle_d28.5895144
NEUTRON DIFFRACTIONf_bond_d0.0116573
NEUTRON DIFFRACTIONf_angle_d1.4385863
NEUTRON DIFFRACTIONf_chiral_restr0.076847
NEUTRON DIFFRACTIONf_plane_restr0.011846
NEUTRON DIFFRACTIONf_dihedral_angle_d28.5895144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.020.25891630.1866989X-RAY DIFFRACTION83.42
1.02-1.040.20561660.1991053X-RAY DIFFRACTION84.54
1.04-1.060.16691680.17141111X-RAY DIFFRACTION88.39
1.06-1.090.16571266X-RAY DIFFRACTION88.1
1.09-1.110.18121710.15121203X-RAY DIFFRACTION93.53
1.11-1.140.15191680.13941140X-RAY DIFFRACTION95.06
1.14-1.180.18391670.14341223X-RAY DIFFRACTION95.53
1.18-1.220.20221210.15241244X-RAY DIFFRACTION96.06
1.22-1.260.1955530.16161315X-RAY DIFFRACTION95.33
1.26-1.310.21181680.17511181X-RAY DIFFRACTION94.6
1.31-1.370.19341700.16821232X-RAY DIFFRACTION98.25
1.37-1.440.24441640.16181265X-RAY DIFFRACTION98.62
1.44-1.530.19141680.16721250X-RAY DIFFRACTION98.27
1.53-1.650.1565560.15721359X-RAY DIFFRACTION99.37
1.65-1.820.15971180.15631315X-RAY DIFFRACTION99.72
1.82-2.080.17441700.1481256X-RAY DIFFRACTION99.44
2.08-2.620.16531590.16311269X-RAY DIFFRACTION99.72
2.62-16.630.17641570.12961259X-RAY DIFFRACTION98.68

+
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