[English] 日本語
Yorodumi
- PDB-3mbs: Crystal structure of 8mer PNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mbs
TitleCrystal structure of 8mer PNA
ComponentsPeptide Nucleic Acid
KeywordsPeptide Nucleic Acid / Peptide Nucleic Acid PNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.27 Å
AuthorsYeh, J.I. / Pohl, E. / Truan, D. / He, W. / Sheldrick, G.M. / Achim, C.
CitationJournal: Chemistry / Year: 2010
Title: The crystal structure of non-modified and bipyridine-modified PNA duplexes.
Authors: Yeh, J.I. / Pohl, E. / Truan, D. / He, W. / Sheldrick, G.M. / Du, S. / Achim, C.
History
DepositionMar 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Dec 11, 2019Group: Advisory / Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn / struct_conn_type
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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: Peptide Nucleic Acid
B: Peptide Nucleic Acid
C: Peptide Nucleic Acid
D: Peptide Nucleic Acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3569
Polymers9,0454
Non-polymers3105
Water4,468248
1
A: Peptide Nucleic Acid
B: Peptide Nucleic Acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7095
Polymers4,5232
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peptide Nucleic Acid
D: Peptide Nucleic Acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6474
Polymers4,5232
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.870, 28.920, 54.970
Angle α, β, γ (deg.)88.10, 85.75, 79.56
Int Tables number1
Space group name H-MP1

-
Components

#1: DNA chain
Peptide Nucleic Acid


Mass: 2261.329 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The molecule has been synthesized
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growMethod: vapor diffusion / pH: 6.2
Details: 40% ethylenglycol 0.1 M Na/K/phosphate, pH 6.2, VAPOR DIFFUSION, temperature RTK

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.8266
SYNCHROTRONSLS X10SA20.8266
SYNCHROTRONAPS 23-ID-B31
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.82661
211
ReflectionResolution: 1.27→50 Å / Num. all: 30089 / Num. obs: 25324 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.2

-
Processing

Software
NameClassification
SHELXSphasing
SHELXDphasing
ACORNphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.27→18.51 Å / Cross valid method: thoughout / σ(F): 4 / σ(I): -3 / Details: conjugate gradient refinement against I
RfactorNum. reflectionSelection details
Rfree0.22 1547 random
Rwork0.179 --
obs0.179 25324 -
all-29399 -
Refinement stepCycle: LAST / Resolution: 1.27→18.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms624 0 20 248 892

+
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