[English] 日本語
Yorodumi
- PDB-1ilc: DNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ilc
TitleDNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regulation.
Components5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
KeywordsDNA / B-DNA DOUBLE HELIX / DODECAMER DUPLEX / HPV E2 DNA TARGET
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHizver, J. / Rozenberg, H. / Frolow, F. / Rabinovich, D. / Shakked, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: DNA bending by an adenine--thymine tract and its role in gene regulation.
Authors: Hizver, J. / Rozenberg, H. / Frolow, F. / Rabinovich, D. / Shakked, Z.
History
DepositionMay 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
B: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
C: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
D: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
E: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
F: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)21,9746
Polymers21,9746
Non-polymers00
Water2,054114
1
A: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
B: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
D: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'
F: 5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.821, 40.160, 39.460
Angle α, β, γ (deg.)74.42, 76.44, 59.90
Int Tables number1
Space group name H-MP1

-
Components

#1: DNA chain
5'-D(*AP*CP*CP*GP*AP*AP*TP*TP*CP*GP*GP*T)-3'


Mass: 3662.404 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Human papillomavirus E2 DNA target
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.29 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, magnesium chloride, spermine.4HCl, Na cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Mg2Cl11
3spermine.4HCl11
4Na cacodylate11
5MPD12
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 mg/mlDNA1drop
276 mM1dropMgCl2
31 mMspermine-4HCl1drop
420 mMsodium cacodylate1droppH7.0
515 %(w/v)1drop
637 %(w/v)MPD1reservoir
720 mMsodium cacodylate1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 10, 1997 / Details: Yale-type mirrors
RadiationMonochromator: Ni filter + Yale-type mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19 Å / Num. all: 9810 / Num. obs: 9810 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 25.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2 / Num. unique all: 491 / Rsym value: 0.654 / % possible all: 95
Reflection
*PLUS
Num. measured all: 36389 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 95 % / Rmerge(I) obs: 0.564

-
Processing

Software
NameVersionClassification
MFTmodel building
ULTIMAmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MFTphasing
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fiber model of B-DNA

Resolution: 2.2→19 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al.
Details: REFINEMENT STARTED WITH X-PLOR 3.1 USING B-DNA FIBER MODEL ALL DATA INCLUDED. REFINEMENT CONTINUED IN SHELXL-97 WITH THE OPTION HOPE FOR ANISOTROPIC SCALING TO CORRECT SIGNIFICANT ANISOTROPY ...Details: REFINEMENT STARTED WITH X-PLOR 3.1 USING B-DNA FIBER MODEL ALL DATA INCLUDED. REFINEMENT CONTINUED IN SHELXL-97 WITH THE OPTION HOPE FOR ANISOTROPIC SCALING TO CORRECT SIGNIFICANT ANISOTROPY IN THE DATA. THE CORRECTED OBSERVED STRUCTURE FACTORS WITH F<0 WERE EXCLUDED FROM REFINEMENT. REFINEMENT FURTHER CONTINUED WITH X-PLOR 3.1.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 456 -random
Rwork0.222 ---
obs0.224 8475 86.4 %-
all-9810 --
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1458 0 114 1572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d17.7
LS refinement shellResolution: 2.2→2.3 Å /
RfactorNum. reflection
Rfree0.37 37
Rwork0.33 -
Xplor fileSerial no: 1 / Param file: PARAM_NDBX.DNA / Topol file: TOP_NDBX.DNA
Refinement
*PLUS
Num. reflection obs: 8474 / % reflection Rfree: 5 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / Rfactor Rwork: 0.33 / Rfactor obs: 0.33

+
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