[English] 日本語
Yorodumi
- PDB-1ih3: Multi-conformation crystal structure of GGm5CGm5CC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ih3
TitleMulti-conformation crystal structure of GGm5CGm5CC
Components5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
KeywordsDNA / B to A DNA transition / DNA transition / structural transition
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVargason, J.M. / Henderson, K. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A crystallographic map of the transition from B-DNA to A-DNA.
Authors: Vargason, J.M. / Henderson, K. / Ho, P.S.
History
DepositionApr 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
B: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
C: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
D: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
E: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
F: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
G: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
H: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'


Theoretical massNumber of molelcules
Total (without water)14,7068
Polymers14,7068
Non-polymers00
Water1,31573
1
A: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
B: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,6772
Polymers3,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
D: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,6772
Polymers3,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
F: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,6772
Polymers3,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'
H: 5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'


Theoretical massNumber of molelcules
Total (without water)3,6772
Polymers3,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.345, 42.345, 179.399
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: DNA chain
5'-D(*GP*GP*(5CM)P*GP*(5CM)P*C)-3'


Mass: 1838.259 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 4.61 Å3/Da / Density % sol: 73.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: magnesium chloride, sodium cacodylate, spermine tetrahydrochloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2sodium cacodylate11
3spermine tetrahydrochloride11
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.7 mMDNA1drop
225 mM1drop
30.8 mM1dropMgCl2
40.1-1.2 mMspermine tetrahydrochloride1drop
515 %(v/v)MPD1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 8, 1999
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 7273 / Num. obs: 7273 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 30.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.353 / % possible all: 61.5
Reflection
*PLUS
Num. measured all: 49399 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 61.5 % / Rmerge(I) obs: 0.4

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: G.Parkinson, J.Vojtechovsky, L.Clowney, A.T.Brunger, H.M.Berman
RfactorNum. reflectionSelection details
Rfree0.2 325 Random
Rwork0.173 --
all0.198 7269 -
obs0.198 7269 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 960 16 73 1049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.82
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.173 / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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