[English] 日本語
Yorodumi
- PDB-1pnn: PEPTIDE NUCLEIC ACID (PNA) COMPLEXED WITH DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pnn
TitlePEPTIDE NUCLEIC ACID (PNA) COMPLEXED WITH DNA
Components
  • DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
  • PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH)
KeywordsPEPTIDE NUCLEIC ACID/DNA / HAIRPIN PNA:DNA TRIPLEX / TRIPLEX WATSON-CRICK HOOGSTEEN / PEPTIDE NUCLEIC ACID-DNA COMPLEX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBetts, L. / Veal, J.M.
Citation
Journal: Science / Year: 1995
Title: A Nucleic Acid Triple Helix Formed by a Peptide Nucleic Acid-DNA Complex
Authors: Betts, L. / Josey, J.A. / Veal, J.M. / Jordan, S.R.
#1: Journal: Science / Year: 1994
Title: NMR Solution Structure of a Peptide Nucleic Acid Complexed with RNA
Authors: Brown, S.C. / Thomson, S.A. / Veal, J.M. / Davis, D.G.
History
DepositionOct 13, 1995Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH)
B: DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
C: PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH)
D: DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)16,3204
Polymers16,3204
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.380, 73.380, 141.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.545117, -0.361267, -0.756527), (-0.305617, -0.754662, 0.580589), (-0.78067, 0.547697, 0.300969)
Vector: 55.7967, 73.526, 1.5171)

-
Components

#1: DNA chain PNA (NH2-P(*C*T*C*T*T*C*T*T*C-HIS-GLY-SER-SER-GLY-HIS-C*T*T*C*T*T*C*T*C)-COOH) / HAIRPIN PNA:DNA TRIPLEX


Mass: 5322.071 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Mass: 2837.900 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CRYSTALLIZED FROM AMMONIUM SULFATE AND TRIS PH 8.5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growpH: 8.5 / Details: pH 8.5

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.978
ROTATING ANODE21.5418
Detector
TypeIDDetectorDate
1CCDMay 8, 1994
RIGAKU RAXIS IIC2IMAGE PLATEJan 11, 1994
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
21.54181
ReflectionResolution: 2.5→20 Å / Num. obs: 8374 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.043

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
RefinementResolution: 2.5→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.235 --
Rwork0.187 --
obs0.187 6857 95 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 380 0 35 1165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.43
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d6.75
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://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