[English] 日本語
Yorodumi
- PDB-4c5x: Ultra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c5x
TitleUltra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydroxymethyl-cytosine Modification
Components5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3'
KeywordsDNA / CYTOSINE MODIFICATION
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMcDonough, M. / El-Sagheer, A.H. / Brown, T. / Schofield, C.J.
CitationJournal: Chem. Commun. (Camb.) / Year: 2014
Title: Structural insights into how 5-hydroxymethylation influences transcription factor binding.
Authors: Lercher, L. / McDonough, M.A. / El-Sagheer, A.H. / Thalhammer, A. / Kriaucionis, S. / Brown, T. / Schofield, C.J.
History
DepositionSep 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3'
B: 5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4113
Polymers7,3872
Non-polymers241
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6.7 kcal/mol
Surface area4590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.300, 40.270, 64.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 3693.418 Da / Num. of mol.: 2 / Fragment: DICKERSON-DREW SEQUENCE DODECAMER / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.5
Details: 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2011 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.21→34.22 Å / Num. obs: 19814 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 15.58 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 26.2
Reflection shellResolution: 1.21→1.24 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / % possible all: 79.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENRTY 1BNA

1bna


Resolution: 1.3→34.2 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 16.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1734 2971 10.15 %
Rwork0.1421 --
obs0.1452 17362 93.78 %
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.272 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso mean: 22.06 Å2
Baniso -1Baniso -2Baniso -3
1-7.7695 Å20 Å20 Å2
2---6.7934 Å20 Å2
3----0.9761 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 1 136 627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022555
X-RAY DIFFRACTIONf_angle_d2.486858
X-RAY DIFFRACTIONf_dihedral_angle_d30.11226
X-RAY DIFFRACTIONf_chiral_restr0.12494
X-RAY DIFFRACTIONf_plane_restr0.04124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32130.22611300.19481167X-RAY DIFFRACTION84
1.3213-1.34410.21341210.18551149X-RAY DIFFRACTION85
1.3441-1.36850.22851360.18091180X-RAY DIFFRACTION89
1.3685-1.39490.23931370.16211240X-RAY DIFFRACTION91
1.3949-1.42330.22421350.16641214X-RAY DIFFRACTION92
1.4233-1.45430.20221420.15031259X-RAY DIFFRACTION94
1.4543-1.48810.23971470.15951296X-RAY DIFFRACTION94
1.4881-1.52530.18851390.14011201X-RAY DIFFRACTION91
1.5253-1.56660.19471410.11951300X-RAY DIFFRACTION96
1.5666-1.61270.16271460.11291291X-RAY DIFFRACTION95
1.6127-1.66470.12611440.10011284X-RAY DIFFRACTION95
1.6647-1.72420.15371420.09791299X-RAY DIFFRACTION97
1.7242-1.79320.13311490.10651330X-RAY DIFFRACTION97
1.7932-1.87490.17951460.12431312X-RAY DIFFRACTION98
1.8749-1.97370.19211470.12941322X-RAY DIFFRACTION98
1.9737-2.09730.15721410.13251237X-RAY DIFFRACTION92
2.0973-2.25920.19521480.13571318X-RAY DIFFRACTION98
2.2592-2.48650.20071460.16551324X-RAY DIFFRACTION97
2.4865-2.84620.19171490.15051300X-RAY DIFFRACTION97
2.8462-3.58530.16641410.16451286X-RAY DIFFRACTION95
3.5853-34.22690.14321440.13851288X-RAY DIFFRACTION96

+
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