[English] 日本語
Yorodumi
- PDB-3iki: 5-SMe-dU containing DNA octamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iki
Title5-SMe-dU containing DNA octamer
Components5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'
KeywordsDNA / Selenium / Nucleic Acid / 5-SMe-deoxyuridine / 2'-SeMe-deoxyuridine
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsSheng, J. / Hassan, A.E.A. / Zhang, W. / Gan, J. / Huang, Z.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.
Authors: Sheng, J. / Zhang, W. / Hassan, A.E. / Gan, J. / Soares, A.S. / Geng, S. / Ren, Y. / Huang, Z.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 13, 2012Group: Database references
Revision 1.3Sep 26, 2012Group: Database references
Revision 1.4Sep 6, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5622
Polymers2,5381
Non-polymers241
Water68538
1
A: 5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'
hetero molecules

A: 5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1244
Polymers5,0752
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2240 Å2
ΔGint-12 kcal/mol
Surface area2810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.882, 42.882, 23.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: DNA chain 5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'


Mass: 2537.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by solid phase synthesis
#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.: 38 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v / v MPD, 40 mM Na Cacodylate pH 7.0, 12 mM Spermine tetra-HCl, 40 mM Lithium Chloride, 80 mM Strontium Chloride / 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2008
RadiationMonochromator: channel-cut Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 4911 / Num. obs: 4616 / % possible obs: 94 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.02
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 5.86 / Num. unique all: 324 / % possible all: 67.8

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DNS

1dns


Resolution: 1.38→30.32 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.592 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19414 216 4.7 %RANDOM
Rwork0.17838 ---
all0.17907 4650 --
obs-4373 94.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.06 Å0.061 Å
Refinement stepCycle: LAST / Resolution: 1.38→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 163 1 38 202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021180
X-RAY DIFFRACTIONr_angle_refined_deg1.4673270
X-RAY DIFFRACTIONr_chiral_restr0.0570.231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0283
X-RAY DIFFRACTIONr_nbd_refined0.3710.266
X-RAY DIFFRACTIONr_nbtor_refined0.2770.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.210
X-RAY DIFFRACTIONr_scbond_it0.8253261
X-RAY DIFFRACTIONr_scangle_it1.2494.5270
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 14 -
Rwork0.203 216 -
obs--65.53 %
Refinement TLS params.Method: refined / Origin x: 31.5133 Å / Origin y: 30.4882 Å / Origin z: 2.3842 Å
111213212223313233
T0.0169 Å2-0.0065 Å20.0054 Å2--0.0057 Å2-0.0025 Å2--0.0077 Å2
L0.1824 °2-0.3805 °2-0.0034 °2-1.305 °20.2072 °2--0.2928 °2
S-0.0049 Å °0.0122 Å °0.0094 Å °0.1295 Å °0.0189 Å °-0.0139 Å °0.0248 Å °-0.0403 Å °-0.014 Å °

+
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