[English] 日本語
Yorodumi
- PDB-1zf5: GCT duplex B-DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zf5
TitleGCT duplex B-DNA
Components5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'
KeywordsDNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsHays, F.A. / Teegarden, A.T. / Jones, Z.J.R. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: How sequence defines structure: a crystallographic map of DNA structure and conformation.
Authors: Hays, F.A. / Teegarden, A. / Jones, Z.J. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
History
DepositionApr 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,0461
Polymers3,0461
Non-polymers00
Water00
1
A: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'

A: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)31.687, 25.721, 34.089
Angle α, β, γ (deg.)90.00, 116.71, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: DNA chain 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY ...Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 298 K / pH: 7
Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1Na Cacodylate11
2CaCl211
3Spermine11
4MPD11
5H2O11
6Na Cacodylate12
7CaCl212
8MPD12
9H2O12

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 0.99→11.07 Å / Num. obs: 12303 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 0.7 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 27.4
Reflection shellResolution: 0.99→1.03 Å / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.161 / % possible all: 43.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0003refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.99→11.07 Å / Cor.coef. Fo:Fc: 0.825 / Cor.coef. Fo:Fc free: 0.849 / SU B: 0.529 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: STRUCTURE IS NOT REFINED TO ITS LOWEST R VALUES, REFER TO CITATION. ALTERNATE CONFORMATIONS CLEARLY VISIBLE ALONG DNA BACKBONE.`
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1260 10.3 %RANDOM
Rwork0.29 ---
obs-12191 88.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT MODEL
Displacement parametersBiso mean: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.05 Å2
2--0.31 Å20 Å2
3---0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: -0.08 Å
Refinement stepCycle: LAST / Resolution: 0.99→11.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 0 202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.021226
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg13347
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.239
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02104
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.294
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it0.5053330
X-RAY DIFFRACTIONr_scangle_it0.8424.5347
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.99→1.05 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 104 -
Rwork0.287 1008 -
obs--48.9 %

+
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