[English] 日本語
Yorodumi
- PDB-1rru: The influence of a chiral amino acid on the helical handedness of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rru
TitleThe influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals
ComponentsPeptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)
KeywordsPEPTIDE NUCLEIC ACID / PNA / L-Lysine / helical handedness / P-form / molecular mechanics
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRasmussen, H. / Liljefors, T. / Petersson, B. / Nielsen, P.E. / Kastrup, J.S.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 2004
Title: The Influence of a Chiral Amino Acid on the Helical Handedness of PNA in Solution and in Crystals
Authors: Rasmussen, H. / Liljefors, T. / Petersson, B. / Nielsen, P.E. / Kastrup, J.S.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution
Authors: Rasmussen, H. / Kastrup, J.S. / Nielsen, J.N. / Nielsen, J.M. / Nielsen, P.E.
#2: Journal: New J.Chem. / Year: 1999
Title: Peptide nucleic acids (PNA) derived from N-(N-methylaminoethyl) glycine. Synthesis, hybridization and structural properties
Authors: Haiima, G. / Rasmussen, H. / Schmidt, G. / Jensen, D.K. / Kastrup, J.S. / Stafshede, P.W. / Norden, B. / Buckhardt, O. / Nielsen, P.E.
#3: Journal: Eur.J.Org.Chem. / Year: 2001
Title: 1,8-Naphthyridin-2(1H)-ones. Novel bi- and tricyclic analogues of Thymine in Peptide nucleic acids (PNA)
Authors: Eldrup, A.B. / Nielsen, B.B. / Haiima, G. / Rasmussen, H. / Kastrup, J.S. / Christensen, C. / Nielsen, P.E.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 28, 2019Group: Data collection / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_biol / struct_conn
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _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: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)
B: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)3,4302
Polymers3,4302
Non-polymers00
Water50428
1
A: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)

A: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)3,4302
Polymers3,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)

B: Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)3,4302
Polymers3,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)36.75, 44.07, 31.22
Angle α, β, γ (deg.)90.00, 91.51, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: DNA chain Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2) / PNA


Mass: 1714.813 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: glycerol, magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1glycerol11
2magnesium formate11
3H2O11
4magnesium formate12
5H2O12

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 16, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. all: 2069 / Num. obs: 2069 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.2 / Num. unique all: 92 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PUP

1pup


Resolution: 2.35→6 Å / Isotropic thermal model: isotropic / Cross valid method: troughout / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: Own parameter and topology file created
RfactorNum. reflection% reflectionSelection details
Rfree0.292 129 -random
Rwork0.219 ---
all-1955 --
obs-1453 74 %-
Displacement parametersBiso mean: 38.4 Å2
Refinement stepCycle: LAST / Resolution: 2.35→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms254 0 0 28 282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_angle_deg3.5
LS refinement shellResolution: 2.35→2.45 Å /
RfactorNum. reflection
Rfree0.366 15
Rwork0.321 -

+
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