[English] 日本語
Yorodumi
- PDB-5mvp: Crystal structure of an A-DNA dodecamer containing the GGGCCC motif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mvp
TitleCrystal structure of an A-DNA dodecamer containing the GGGCCC motif
ComponentsDNA
KeywordsDNA / A-DNA / Unmodified / Self-complementary
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.606 Å
AuthorsHardwick, J.S. / Ptchelkine, D. / Phillips, S.E.V. / Brown, T.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J001694/2
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: 5-Formylcytosine does not change the global structure of DNA.
Authors: Hardwick, J.S. / Ptchelkine, D. / El-Sagheer, A.H. / Tear, I. / Singleton, D. / Phillips, S.E.V. / Lane, A.N. / Brown, T.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.6Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3663
Polymers7,3272
Non-polymers391
Water1,35175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.256, 43.256, 61.552
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: DNA chain DNA /


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium chloride (80 mM) Potassium chloride (12 mM) Magnesium chloride (20 mM) Spermine tetrahydrochloride (12 mM) Sodium cacodylate (40 mM, pH 7.0) MPD (45% v/v)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.606→37.461 Å / Num. obs: 9111 / % possible obs: 99.7 % / Redundancy: 6.3 % / Net I/σ(I): 23

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MVL

5mvl


Resolution: 1.606→37.461 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.97
RfactorNum. reflection% reflection
Rfree0.2089 456 5.02 %
Rwork0.153 --
obs0.1557 9075 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.606→37.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 75 562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014544
X-RAY DIFFRACTIONf_angle_d1.19836
X-RAY DIFFRACTIONf_dihedral_angle_d12.909232
X-RAY DIFFRACTIONf_chiral_restr0.08194
X-RAY DIFFRACTIONf_plane_restr0.01124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6056-1.8380.23851670.20092776X-RAY DIFFRACTION99
1.838-2.31560.26231510.19472848X-RAY DIFFRACTION100
2.3156-37.4710.19291380.14012995X-RAY DIFFRACTION100

+
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