[English] 日本語
Yorodumi
- PDB-1fhz: PSORALEN CROSS-LINKED D(CCGGTACCGG) FORMS HOLLIDAY JUNCTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fhz
TitlePSORALEN CROSS-LINKED D(CCGGTACCGG) FORMS HOLLIDAY JUNCTION
ComponentsDNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
KeywordsDNA / psoralen / cross-linked DNA / Holliday junction / DNA-drug complex
Function / homology4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEichman, B.F. / Mooers, B.H.M. / Alberti, M. / Hearst, J.E. / Ho, P.S.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions.
Authors: Eichman, B.F. / Mooers, B.H. / Alberti, M. / Hearst, J.E. / Ho, P.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions
Authors: Eichman, B.F. / Vargason, J.M. / Mooers, B.H.M. / Ho, P.S.
History
DepositionAug 2, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,3503
Polymers6,0922
Non-polymers2581
Water77543
1
A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7016
Polymers12,1844
Non-polymers5172
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)72.116, 23.651, 36.182
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-62-

HOH

DetailsA four-way junction is a dimer constructed from chains A and B and a symmetry partner generated by the two-fold

-
Components

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


Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA IS CROSS-LINKED BY PSORALEN
#2: Chemical ChemComp-PSO / 4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN


Mass: 258.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium cacodylate, MgCl2, MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2MgCl211
3MPD11
4MgCl212
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mM1drop
20.5 mMDNA1drop
350 mM1dropCaCl2
410 %MPD1drop
520 %(v/v)1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→33.39 Å / Num. all: 2900 / Num. obs: 2900 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Num. unique all: 284 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 33.4 Å / Num. measured all: 9596
Reflection shell
*PLUS
% possible obs: 98.3 % / Mean I/σ(I) obs: 8.1

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33.39 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Parkinson et al.
Details: ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
RfactorNum. reflection% reflectionSelection details
Rfree0.311 305 10.5 %random
Rwork0.228 ---
all0.236 2891 --
obs0.236 2891 96.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.0249 Å20 Å2-0.0139 Å2
2--13.3859 Å20 Å2
3----5.361 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 19 43 466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg1.594
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 33.4 Å / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.229

+
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