[English] 日本語
Yorodumi
- PDB-1en3: 1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1en3
Title1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM
ComponentsDNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
KeywordsDNA / DIVALENT CATIONS / DNA SEQUENCE-SPECIFIC BINDING / SHELXDNA / B-DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.985 Å
AuthorsChiu, T.K. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium.
Authors: Chiu, T.K. / Dickerson, R.E.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG.
Authors: Chiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
History
DepositionMar 20, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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 / 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.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1425
Polymers3,0451
Non-polymers974
Water1,36976
1
A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,28410
Polymers6,0902
Non-polymers1948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)32.001, 25.369, 33.633
Angle α, β, γ (deg.)90.00, 112.98, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-111-

MG

21A-217-

HOH

31A-219-

HOH

-
Components

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


Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.08 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop
Details: INITIAL CONCENTRATION IN DROPLET: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% FINAL MPD CONCENTRATION IN RESERVOIR. SOLUTIONS WERE UNBUFFERED, VAPOR ...Details: INITIAL CONCENTRATION IN DROPLET: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% FINAL MPD CONCENTRATION IN RESERVOIR. SOLUTIONS WERE UNBUFFERED, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM ACETATE11
2STREPTONIGRIN11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.24 mMduplex DNA1drop
28.57 mMdivalent cation1drop
30.11 mMstreptonigrin1drop
445 %1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 0.985→8 Å / Num. all: 13464 / Num. obs: 13464 / % possible obs: 95 % / Observed criterion σ(I): -1 / Redundancy: 5.75 % / Biso Wilson estimate: 5.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.6
Reflection shellResolution: 0.985→1.016 Å / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 7.4 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 77354
Reflection shell
*PLUS
% possible obs: 90.7 %

-
Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BDJ019

Resolution: 0.985→8 Å / Num. parameters: 17441 / Num. restraintsaints: 2945 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL.
Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT ...Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT LEAST-SQUARES IN SHELXL-97. THE TOP 50 MOST DISAGREEABLE REFLECTIONS WERE REJECTED TOWARDS THE LATTER STAGES OF REFINEMENT BUT THESE ARE STILL INCLUDED IN THE RELEASED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.1592 631 5 %RANDOM
Rwork0.1409 ---
obs0.1409 13464 95 %-
all-13464 --
Solvent computationSolvent model: SWAT 0.814695 0.4550
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 114 / Occupancy sum non hydrogen: 272.84
Refinement stepCycle: LAST / Resolution: 0.985→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 364 32 61 457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.049
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0.072
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.033
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.2395 / Rfactor Rwork: 0.1529

+
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