[English] 日本語
Yorodumi
- PDB-392d: STRUCTURAL VARIABILITY AND NEW INTERMOLECULAR INTERACTIONS OF Z-D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 392d
TitleSTRUCTURAL VARIABILITY AND NEW INTERMOLECULAR INTERACTIONS OF Z-DNA IN CRYSTALS OF D(PCPGPCPGPCPG)
ComponentsDNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsMalinina, L. / Tereshko, V. / Ivanova, E. / Subirana, J.A. / Zarytova, V. / Nekrasov, Y.
Citation
Journal: Biophys.J. / Year: 1998
Title: Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG).
Authors: Malinina, L. / Tereshko, V. / Ivanova, E. / Subirana, J.A. / Zarytova, V. / Nekrasov, Y.
#1: Journal: J.Biomol.Struct.Dyn. / Year: 1994
Title: A Simplified Multidimensional Search Used for Crystal Structure Sloution of pCpGpCpGpCpG with Two Duplexes per Asymmetric Unit
Authors: Strocopytov, B.V. / Malinina, L.V.
History
DepositionApr 20, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0May 5, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 21, 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.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_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(P*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2655
Polymers7,2414
Non-polymers241
Water00
1
A: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6453
Polymers3,6202
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.800, 37.300, 70.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 1810.205 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growpH: 6 / Details: pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MGCL211
3SPERMINE TETRACLORIDE11
4NA CACODYLATE11
52-METHYL-2,4-PENTANEDIOL11
6WATER12
72-METHYL-2,4-PENTANEDIOL12
Crystal grow
*PLUS
Method: other / Details: Malinina, L., (1991) J. Crystal Growth, 110, 252.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51
61
71

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER / Date: Jan 1, 1988
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→35.2 Å / Num. obs: 1276 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.08

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
SYNTEXP21data reduction
SYNTEXP21data scaling
RefinementResolution: 3→8 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.182 ---
all0.188 1189 --
obs0.182 1144 92.1 %-
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 496 1 0 497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.57
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

+
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