[English] 日本語
Yorodumi
- PDB-2b1c: 5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3' Zif268 binding site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b1c
Title5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3' Zif268 binding site
Components
  • 5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3'
  • 5'-D(*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3'
KeywordsDNA / sequence dependent DNA deformation / A form DNA / protein-DNA recognition
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBerman, H.M. / Napoli, A.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Signatures of protein-DNA recognition in free DNA binding sites.
Authors: Locasale, J.W. / Napoli, A.A. / Chen, S. / Berman, H.M. / Lawson, C.L.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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: 5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3'
B: 5'-D(*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1163
Polymers6,0922
Non-polymers241
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.482, 38.482, 78.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

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


Mass: 3086.017 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3'


Mass: 3005.969 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / pH: 5.5
Details: MPD, sodium cacodylate, cobalt hexamine, sodium chloride, potassium chloride, vapor diffusion, hanging drop, temperature 295K, pH 5.50
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3cobalt hexamine11
4sodium chloride11
5potassium chloride11
6H2O11
7MPD12
8sodium cacodylate12
9cobalt hexamine12
10sodium chloride12
11potassium chloride12
12H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0067
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0067 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 1752 / % possible obs: 85.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 4.9 / % possible all: 36.2

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å10 Å
Translation3 Å12 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 401D

401d


Resolution: 2.2→30.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.286 165 8.2 %RANDOM
Rwork0.234 ---
obs0.234 1749 87.1 %-
all-1752 --
Solvent computationBsol: 199.44 Å2
Displacement parametersBiso mean: 22.62 Å2
Baniso -1Baniso -2Baniso -3
1--4.928 Å2-13.082 Å20 Å2
2---4.928 Å20 Å2
3---9.856 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.2→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 3 18 425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d10.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4191 8 10 %
Rwork0.4321 89 -
obs--41 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1DNA-RNA_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION4MO2.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://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