[English] 日本語
Yorodumi
- PDB-3gda: Crystal study of d(CACGCG).d(CGCGTG) grwon in presence of stannou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gda
TitleCrystal study of d(CACGCG).d(CGCGTG) grwon in presence of stannous chloride
Components
  • 5'-D(*CP*AP*CP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*GP*TP*G)-3'
KeywordsDNA / Double stranded Z-form DNA with Watson-Crick base pairing
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMandal, P.K. / Venkadesh, S. / Gautham, N.
CitationJournal: To be Published
Title: Crystal structure of d(CACGCG).d(CGCGTG) grown in presence of SnCl2
Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*AP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-6 kcal/mol
Surface area2320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.552, 30.207, 43.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*CP*GP*TP*G)-3'


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: 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: 1

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: Sodium cacodylate 50mM, SnCl2 0.5mM, Spermine 10mM, Methyl pentane diol 33%, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium cacoldylate11
2SnCl211
3Spermine11
4MPD11
5Sodium cacoldylate12
6SnCl212
7MPD12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→12 Å / Num. all: 2132 / Num. obs: 2113 / % possible obs: 99.1 % / Redundancy: 4.05 % / Biso Wilson estimate: 38.47 Å2 / Rmerge(I) obs: 0.0579 / Rsym value: 0.0501 / Net I/σ(I): 6.7
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 4.18 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 1.1 / Num. unique all: 206 / Rsym value: 0.2838 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Z-DNA FIBER MODEL BUILT WITH INSIGHT-II

Resolution: 1.88→10.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.153 / SU ML: 0.111 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26596 107 5.1 %RANDOM
Rwork0.241 ---
obs0.24219 1992 99.62 %-
all-1999 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.88→10.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 19 259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021272
X-RAY DIFFRACTIONr_angle_refined_deg2.0153418
X-RAY DIFFRACTIONr_chiral_restr0.0730.247
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02125
X-RAY DIFFRACTIONr_nbd_refined0.1620.297
X-RAY DIFFRACTIONr_nbtor_refined0.2820.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.23
X-RAY DIFFRACTIONr_scbond_it2.6763398
X-RAY DIFFRACTIONr_scangle_it2.6754.5417
LS refinement shellResolution: 1.875→1.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 8 -
Rwork0.44 146 -
obs-1992 100 %

+
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