[English] 日本語
Yorodumi
- PDB-1ue2: Crystal structure of d(GC38GAAAGCT) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ue2
TitleCrystal structure of d(GC38GAAAGCT)
Components5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3'
KeywordsDNA / base-intercalated duplex / mini-hairpin structure / sheared G:A pair / zipper-like duplex
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / HEAVY-ATOM METHOD / Resolution: 1.4 Å
AuthorsSunami, T. / Kondo, J. / Hirao, I. / Watanaba, K. / Miura, K. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure.
Authors: Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K.I. / Takenaka, A.
History
DepositionMay 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 22, 2014Group: Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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: 5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1124
Polymers2,8911
Non-polymers2213
Water97354
1
A: 5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3'
hetero molecules

A: 5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2238
Polymers5,7812
Non-polymers4426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
Unit cell
Length a, b, c (Å)36.736, 36.736, 64.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-10-

CL

21A-766-

NCO

31A-774-

HOH

41A-775-

HOH

51A-776-

HOH

61A-777-

HOH

-
Components

#1: DNA chain 5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3'


Mass: 2890.734 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.81 Å3/Da / Density % sol: 31.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2,6-diaminopyridine, magnesium chloride, sodium chloride, hexaamminecobalt(III) chloride, 2-methyl-2,4-pentanediol, MEGA-10, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
12,6-diaminopyridine11
2magnesium chloride11
3sodium chloride11
4hexaamminecobalt(III) chloride11
52-methyl-2,4-pentanediol11
6MEGA-1011
7sodium cacodylate11
82,6-diaminopyridine12
9magnesium chloride12
10sodium chloride12
11hexaamminecobalt(III) chloride12
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 mMDNA1drop
29 mM2,6-diaminopyridine1drop
320 mM1reservoirMgCl2
480 mM1reservoirNaCl
530 mM1reservoirCo(HN3)6Cl3
620 %MPD1reservoir
70.17 %n-decanoyl-N-methylglucamide1reservoir
840 mMsodium cacodylate1reservoirpH6.0
91
101
111

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→18 Å / Num. all: 5562 / Num. obs: 5553 / % possible obs: 99.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 6.8
Reflection shellResolution: 1.4→1.43 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.6 / % possible all: 100
Reflection
*PLUS
Num. measured all: 546817
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
CNSrefinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: HEAVY-ATOM METHOD / Resolution: 1.4→10 Å / σ(F): 3
Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
RfactorNum. reflectionSelection details
Rfree0.2357 613 RANDOM
Rwork0.2091 --
all-5512 -
obs-5111 -
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 168 5 54 227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.4→1.45 Å /
RfactorNum. reflection
Rfree0.3202 54
Rwork0.2336 -
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4

+
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