[English] 日本語
Yorodumi
- PDB-4b8d: TENSEGRITY TRIANGLE FROM ENZYMATICALLY MANUFACTURED DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b8d
TitleTENSEGRITY TRIANGLE FROM ENZYMATICALLY MANUFACTURED DNA
Components
  • 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
  • 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
  • 5'-D(*GP*GP*CP*TP*GP*CP)-3'
  • 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'
KeywordsDNA / ROLLING CIRCLE AMPLIFICATION / DNA ORIGAMI
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.79 Å
AuthorsDucani, C. / Kaul, C.D. / Moche, M. / Shih, W.M. / Hogberg, B.
CitationJournal: Nat.Methods / Year: 2013
Title: Enzymatic Production of 'Monoclonal Stoichiometric' Single-Stranded DNA Oligonucleotides
Authors: Ducani, C. / Kaul, C.D. / Moche, M. / Shih, W.M. / Hogberg, B.
History
DepositionAug 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_symm_contact ...pdbx_database_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1
A: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
B: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
C: 5'-D(*GP*GP*CP*TP*GP*CP)-3'
D: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'

A: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
B: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
C: 5'-D(*GP*GP*CP*TP*GP*CP)-3'
D: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'

A: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP *GP*AP*CP*AP*TP*CP*A)-3'
B: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'
C: 5'-D(*GP*GP*CP*TP*GP*CP)-3'
D: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)38,39212
Polymers38,39212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.437, 106.437, 95.154
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

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


Mass: 6457.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
#2: DNA chain 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'


Mass: 2082.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
#3: DNA chain 5'-D(*GP*GP*CP*TP*GP*CP)-3'


Mass: 1825.216 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
#4: DNA chain 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'


Mass: 2432.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
Description: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE -ENZYMATICALLY PRODUCED
Production host: ESCHERICHIA COLI (E. coli)
Compound detailsTHE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD ...THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS ARE: (#1) 3 STRANDS 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP *CP*A)-3' (#2) 1 STRAND 5'-D(*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP* CP*G)-3' (#3) 3 STRANDS 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3' THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #1 STRAND (CHAIN A), 7-RESIDUE REPEATING UNIT OF #2 STRAND (CHAIN B) AND TWO FRAGMENTS OF #3 STRAND (CHAINS C AND D). THE #2 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL REPEATING UNITS. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS ONE OF THESE REPEATING UNITS. CHAINS D (FIRST 8 RESIDUES OF STRAND #3) AND C (NEXT 6 RESIDUES OF STRAND #3) TOGETHER FORM THE THIRD DNA STRAND (#3) OF THE EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT WAS DIVIDED INTO THE CURRENT CHAINS C AND D FOR CONVENIENT REPRESENTATION. CHAIN C (1_555) IS COVALENTLY LINKED TO CHAIN D OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN D (1_555) IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT (2_555). THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN A.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 8.59 Å3/Da / Density % sol: 85.56 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 4.79→42.3 Å / Num. obs: 1980 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 273.09 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 4.79→5.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GBI

3gbi


Resolution: 4.79→42.28 Å / Cor.coef. Fo:Fc: 0.8711 / Cor.coef. Fo:Fc free: 0.8744 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.644
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=0. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=861. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=0. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=861. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 185 9.34 %RANDOM
Rwork0.1848 ---
obs0.1872 1980 99.6 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-65.6198 Å20 Å20 Å2
2--65.6198 Å20 Å2
3----131.2396 Å2
Refine analyzeLuzzati coordinate error obs: 0.672 Å
Refinement stepCycle: LAST / Resolution: 4.79→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 863 0 0 863
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01988HARMONIC2
X-RAY DIFFRACTIONt_angle_deg2.461517HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d514SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes42HARMONIC5
X-RAY DIFFRACTIONt_it988HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion29.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion130SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1014SEMIHARMONIC4
LS refinement shellResolution: 4.79→5.36 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2933 49 8.78 %
Rwork0.2433 509 -
all0.2475 558 -
obs--99.6 %

+
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