[English] 日本語
Yorodumi
- PDB-2xc6: Crystal structure of the GNA 3'-CTC(Br)UAGAG-2' -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xc6
TitleCrystal structure of the GNA 3'-CTC(Br)UAGAG-2'
ComponentsGNA
KeywordsRNA / WATSON-CRICK BASE PAIR / GLYCOL NUCLEIC ACID
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsSchlegel, M.K. / Essen, L.-O. / Meggers, E.
Citation
Journal: J.Org.Chem. / Year: 2011
Title: On the Structure and Dynamics of Duplex Gna.
Authors: Johnson, A.T. / Schlegel, M.K. / Meggers, E. / Essen, L.O. / Wiest, O.
#1: Journal: J.Am.Chem.Soc. / Year: 2008
Title: Duplex Structure of a Minimal Nucleic Acid.
Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E.
#2: Journal: Chem.Commun.(Camb.) / Year: 2010
Title: Atomic Resolution Duplex Structure of the Simplified Nucleic Acid Gna.
Authors: Schlegel, M.K. / Essen, L.-O. / Meggers, E.
History
DepositionApr 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 2.0Jun 22, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_poly / pdbx_database_status / struct_conn / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2013
Polymers2,1551
Non-polymers462
Water37821
1
A: GNA
hetero molecules

A: GNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4026
Polymers4,3102
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_554y,x,-z-11
Unit cell
Length a, b, c (Å)56.930, 56.930, 28.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: RNA chain GNA


Mass: 2155.194 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SYNTHETIC GLYCOL NUCLEIC ACID 3'-((ZCY)P(ZTH)P(ZCY)P(ZBU)P(ZAD)P(ZGU)P(ZAD)P(ZGU))-2'
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsURACIL U4 IS BROMINATED AT C5 FOR MAD ANALYSIS AT BROMINE EDGE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 5.5
Details: 10 % MPD, 40 MM SODIUM CACODYLATE, PH 5.5, 20 MM COBALT HEXAMINE, 40 MM LICL, 20 MM MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91985
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 24, 2007 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91985 Å / Relative weight: 1
ReflectionResolution: 1.83→15.88 Å / Num. obs: 2242 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 17.4 % / Biso Wilson estimate: 34.172 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.2
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 8.9 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
SHELXEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.83→8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.649 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GNA DUPLEX OF TYPE N FORMED WITH SYMMETRY-EQUIVALENT MOLECULE, 3'TERMINAL CYTOSINE NUCLEOTIDE AND 5-BROMO ATOM AT U4 ONLY PARTIAL OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2706 155 7 %RANDOM
Rwork0.23447 ---
obs0.23697 2068 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.623 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2--1.03 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.83→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 137 2 21 160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021169
X-RAY DIFFRACTIONr_bond_other_d0.0020.0268
X-RAY DIFFRACTIONr_angle_refined_deg1.7153213
X-RAY DIFFRACTIONr_angle_other_deg0.6313154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0284
X-RAY DIFFRACTIONr_gen_planes_other00.0228
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0643148
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9514.5206
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.832→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 11 -
Rwork0.268 138 -
obs--96.75 %
Refinement TLS params.Method: refined / Origin x: 5.0237 Å / Origin y: 6.2082 Å / Origin z: -12.2048 Å
111213212223313233
T0.0841 Å2-0.077 Å20.0458 Å2-0.1045 Å2-0.0241 Å2--0.0904 Å2
L2.061 °20.4823 °22.3312 °2-1.8936 °2-0.6942 °2--4.7135 °2
S0.044 Å °-0.3067 Å °0.055 Å °-0.1721 Å °0.0186 Å °-0.0678 Å °-0.7083 Å °0.6294 Å °-0.0626 Å °

+
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