[English] 日本語
Yorodumi
- PDB-3pbx: Strontium bound to the sequence d(CCGGCGCCGG) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pbx
TitleStrontium bound to the sequence d(CCGGCGCCGG)
ComponentsDNA
KeywordsDNA / Holliday junction (higher order DNA structure) / Intermediate formed in Homologous recombination
Function / homologySTRONTIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.879 Å
AuthorsNaseer, A. / Cardin, C.J.
CitationJournal: To be Published
Title: Strontium bound to the sequence d(CCGGCGCCGG)
Authors: Naseer, A. / Cardin, C.J.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author / software
Item: _audit_author.name / _citation_author.name / _software.name
Revision 1.3Sep 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.pdbx_dist_value / _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.ptnr2_auth_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: DNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2054
Polymers6,0942
Non-polymers1112
Water1,02757
1
A: DNA
B: DNA
hetero molecules

A: DNA
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4098
Polymers12,1884
Non-polymers2214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3610 Å2
ΔGint-79 kcal/mol
Surface area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.890, 25.001, 37.044
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-36-

HOH

-
Components

#1: DNA chain DNA /


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SrCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Feb 10, 2007 / Details: multi-graded optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.879→14.866 Å / Num. all: 4705 / Num. obs: 3706 / % possible obs: 78.55 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 27.446 Å2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.879→1.927 Å

-
Processing

Software
NameVersionClassification
CrysalisProReddata collection
MOLREPphasing
REFMAC5.2.0005refinement
CrysalisProReddata reduction
CrysalisProReddata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GOJ

3goj


Resolution: 1.879→14.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.747 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32701 175 4.7 %RANDOM
Rwork0.2508 ---
obs0.2544 3531 78.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.446 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å20.31 Å2
2--3.36 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.879→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 2 57 463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021452
X-RAY DIFFRACTIONr_angle_refined_deg3.6663694
X-RAY DIFFRACTIONr_chiral_restr0.150.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02210
X-RAY DIFFRACTIONr_nbd_refined0.2590.2130
X-RAY DIFFRACTIONr_nbtor_refined0.3440.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3890.236
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4340.225
X-RAY DIFFRACTIONr_scbond_it3.0073546
X-RAY DIFFRACTIONr_scangle_it4.0164.5694
LS refinement shellResolution: 1.879→1.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 2 -
Rwork0.477 25 -
obs--7.69 %

+
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