[English] 日本語
Yorodumi
- PDB-4hw1: Multiple Crystal structures of an all-AT DNA dodecamer stabilized... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hw1
TitleMultiple Crystal structures of an all-AT DNA dodecamer stabilized by weak interactions.
ComponentsDNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
KeywordsDNA / Oligonucleotide / weak interactions / B form DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAcosta-Reyes, F. / Subirana, J.A. / Pous, J. / Condom, N. / Malinina, L. / Campos, J.L.
CitationJournal: Biopolymers / Year: 2015
Title: Polymorphic crystal structures of an all-AT DNA dodecamer.
Authors: Acosta-Reyes, F.J. / Subirana, J.A. / Pous, J. / Sanchez-Giraldo, R. / Condom, N. / Baldini, R. / Malinina, L. / Campos, J.L.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
B: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
C: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
D: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6625
Polymers14,6384
Non-polymers241
Water25214
1
A: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
B: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3433
Polymers7,3192
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-10 kcal/mol
Surface area4710 Å2
MethodPISA
2
C: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')
D: DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,3192
Polymers7,3192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.431, 61.155, 80.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: DNA chain
DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3')


Mass: 3659.440 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA oligonucleotide.
#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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Mg, MPD, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 2, 2007 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.099→24.36 Å / Num. all: 2435 / Num. obs: 2433 / % possible obs: 99.6 % / Redundancy: 10.25 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.184 / Net I/σ(I): 9.7952
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
3.1-3.279.750.55344198.99
3.27-3.4610.740.8319199.66
3.46-3.710.490.483151100
3.7-410.650.52921100
4-4.3810.550.32701100
4.38-4.910.540.172431100
4.9-5.6610.270.122261100
5.66-6.939.860.081851100
6.93-9.89.580.051511100
9.8-24.368.30.0488193.65

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: theoretic model of B-DNA

Resolution: 3.1→24.36 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R Free: 0.57 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27659 109 4.5 %RANDOM
Rwork0.26196 ---
obs0.26262 2311 99.42 %-
all-2435 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.486 Å2
Baniso -1Baniso -2Baniso -3
1--7.64 Å2-0 Å20 Å2
2--4.69 Å20 Å2
3---2.94 Å2
Refinement stepCycle: LAST / Resolution: 3.1→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 972 1 14 987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0111088
X-RAY DIFFRACTIONr_bond_other_d0.0010.02556
X-RAY DIFFRACTIONr_angle_refined_deg1.041.1881672
X-RAY DIFFRACTIONr_angle_other_deg6.47831324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg52.71620232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg33.54120192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0360.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.02544
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02184
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.099→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.651 13 -
Rwork0.38 162 -
obs--97.77 %

+
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