[English] 日本語
Yorodumi
- PDB-192d: RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 192d
TitleRECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)
ComponentsDNA (5'-D(*CP*CP*GP*CP*GP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / FLIPPED-OUT BASES
MethodX-RAY DIFFRACTION / Resolution: 1.92 Å
AuthorsMalinina, L. / Urpi, L. / Salas, X. / Huynh-Dinh, T. / Subirana, J.A.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Recombination-like structure of d(CCGCGG).
Authors: Malinina, L. / Urpi, L. / Salas, X. / Huynh-Dinh, T. / Subirana, J.A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 22, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,6433
Polymers3,6202
Non-polymers231
Water68538
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)34.330, 44.040, 38.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-13-

NA

21B-44-

HOH

-
Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.43 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP
Components of the solutions

Crystal-ID: 1

IDNameSol-ID
1WATER1
2MPD1
3SPERMINE1
4TETRA-ARGININE1
5NA CACODYLATE1
6WATER2
7MPD2
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
10.83 mMhexanucleotidedrop
22.8 mMsperminedrop
30.6 mMtetra argininedrop
418 mMsodium ccacodylatedrop
520 %(v/v)MPDdrop
645 %MPDreservoir
7

-
Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: OTHER / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.92 Å / Num. all: 13022 / Num. obs: 2297
Reflection
*PLUS
Highest resolution: 1.92 Å / % possible obs: 96.5 % / Redundancy: 5.7 % / Num. measured all: 13022 / Rmerge(I) obs: 0.056

-
Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.92→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.185 --
Obs0.185 2297 96.5 %
Refine Biso
ClassRefinement-ID
ALL ATOMSX-RAY DIFFRACTION
ALL WATERSX-RAY DIFFRACTION
Refinement stepCycle: LAST / Resolution: 1.92→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 274 1 114 389
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.92 Å / Lowest resolution: 8 Å / σ(F): 2

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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