[English] 日本語
Yorodumi
- PDB-1z5t: Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-amin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z5t
TitleCrystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.
Components5'-D(*CP*GP*CP*GP*AP*AP*(ZDU)P*(ZDU)P*CP*GP*CP*G)-3'
KeywordsDNA / B-DNA / Tl+ / thallium / modified DNA / cations / modified thymine
Function / homologySPERMINE / THALLIUM (I) ION / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMoulaei, T. / Maehigashi, T. / Lountos, G.T. / Komeda, S. / Watkins, D. / Stone, M.P. / Marky, L.A. / Li, J.S. / Gold, B. / Williams, L.D.
CitationJournal: Biochemistry / Year: 2005
Title: Structure of B-DNA with cations tethered in the major groove.
Authors: Moulaei, T. / Maehigashi, T. / Lountos, G.T. / Komeda, S. / Watkins, D. / Stone, M.P. / Marky, L.A. / Li, J.S. / Gold, B. / Williams, L.D.
History
DepositionMar 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*GP*CP*GP*AP*AP*(ZDU)P*(ZDU)P*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*(ZDU)P*(ZDU)P*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,53912
Polymers7,4992
Non-polymers2,04010
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.994, 41.057, 66.339
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*(ZDU)P*(ZDU)P*CP*GP*CP*G)-3'


Mass: 3749.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Dickerson-Drew Dodecamer
#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical
ChemComp-TL / THALLIUM (I) ION / Thallium


Mass: 204.383 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Tl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 295.2 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, cacodylate (pH adjusted using spermine base), spermine acetate, ANAPOE-C12E10 (detergent), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.2K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2cacodylateCacodylic acid11
3spermine acetate11
4ANAPOE-C12E10 (detergent)11
5H2O11
6MPD12
7ANAPOE-C12E10 (detergent)12
8H2O12

-
Data collection

DiffractionMean temperature: 113.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0093 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 8901 / % possible obs: 77.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.044 / Χ2: 0.969
Reflection shellResolution: 1.49→1.54 Å / % possible obs: 9.3 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.555 / Num. measured obs: 204 / Χ2: 0.456 / % possible all: 49.1

-
Phasing

Phasing MRCor.coef. Fo:Fc: 0.709 / Packing: 0.423
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation3 Å15 Ådirect95.7 0
Translation3 Å15 Ågeneral95.7 0

-
Processing

Software
NameClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB entery BDL084

Resolution: 1.6→34.91 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 447402.281 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.01 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 778 10.6 %RANDOM
Rwork0.198 ---
all0.233 7355 --
obs0.233 7355 77.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.017 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.87 Å20 Å20 Å2
2--1.22 Å20 Å2
3----7.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 498 22 106 626
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_angle_deg1.38090
X-RAY DIFFRACTIONc_dihedral_angle_d10
X-RAY DIFFRACTIONc_improper_angle_d1.430
X-RAY DIFFRACTIONc_mcbond_it0
X-RAY DIFFRACTIONc_mcangle_it0
X-RAY DIFFRACTIONc_scbond_it0
X-RAY DIFFRACTIONc_scangle_it0
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.222 26 11.4 %
Rwork0.172 203 -
obs--24.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2dna-rna_tinoush.topdna-rna_rep_tinoush.param
X-RAY DIFFRACTION3water.topwater_rep.param
X-RAY DIFFRACTION4ion2.topion2.param
X-RAY DIFFRACTION5spm.topspm.param

+
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