[English] 日本語
Yorodumi
- PDB-1ixj: Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Du... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ixj
TitleCrystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs
Components5'-D(*GP*CP*GP*AP*AP*AP*GP*CP*T)-3'
KeywordsDNA / Parallel DNA / homo base pairs / parallel-stranded helix / parallel duplex
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSunami, T. / Kondo, J. / Kobuna, T. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Crystal Structure of d(GCGAAAGCT) Containing a Parallel-stranded Duplex with Homo Base Pairs and an Anti-Parallel Duplex with Watson-Crick Base pairs
Authors: Sunami, T. / Kondo, J. / Kobuna, T. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A.
History
DepositionJun 22, 2002Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ... BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). BASES 2-5 FORM A PARALLEL STRANDED DUPLEX WITH HOMO BASE PAIRS WITH BASES 2-5 OF THE STRAND GENERATED BY SYMMETRY OPERATOR 8_666 : 1-Y, 1-X, 1-Z. BASES 6-9 FORM AN ANTIPARALLEL DUPLEX WITH WATSON-CRICK BASE PAIRS WITH BASES 9-6 OF THE STRAND GENERATED BY SYMMETRY OPERATOR 5_655 : 3/2-X,Y,3/4-Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,9754
Polymers2,7651
Non-polymers2103
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.4, 53.4, 54.0
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-10-

MG

21A-12-

NCO

-
Components

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


Mass: 2764.837 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


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


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.03 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
12,6-diaminopyridine11
2MgCl211
3NaCl11
4hexaamminecobalt(III) chloride11
52-methyl-2,4-pentanediol11
6MEGA-1011
7sodium cacodylate11
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mMDNA1drop
224 mM2,6-diaminopyridine1drop
320 mM1reservoirpH6.0MgCl2
480 mM1reservoirNaCl
530 mM1reservoirCo(NH3)6Cl3
625 %MPD1reservoir
70.17 %n-decanoyl-N-methylglucamide1reservoir
840 mMsodium cacodylate1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B11
SYNCHROTRONSPring-8 BL44XU20.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 8, 2000
OXFORD PX2102CCDNov 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91
ReflectionResolution: 2.4→37.9 Å / Num. all: 1689 / Num. obs: 1676 / % possible obs: 100 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.4→2.52 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 2.7 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 27 Å / Num. obs: 1647 / % possible obs: 98.3 % / Num. measured all: 20224
Reflection shell
*PLUS
Lowest resolution: 2.53 Å / % possible obs: 100 % / Rmerge(I) obs: 0.054

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→9 Å / σ(F): 3
Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
Details: The C1*-C2*-C3* angle of the G7 residue is slightly small due to large temperature factor of the C8 residue.
RfactorNum. reflectionSelection details
Rfree0.257 130 RANDOM
Rwork0.215 --
all-1415 -
obs-1333 -
Refinement stepCycle: LAST / Resolution: 2.5→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 184 21 7 212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 2.5→2.61 Å /
RfactorNum. reflection
Rfree0.52 12
Rwork0.413 -
Refinement
*PLUS
Lowest resolution: 9 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3

+
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