[English] 日本語
Yorodumi
- PDB-1cvx: CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cvx
TitleCRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG
Components5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'
KeywordsDNA / POLYAMIDE / MINOR GROOVE RECOGNITION / TA RECOGNITION / DOUBLE DRUG IN MINOR GROOVE
Function / homologyHYDROXYPYRROLE-IMIDAZOLE-PYRROLE POLYAMIDE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.27 Å
AuthorsKielkopf, C.L. / Bremer, R.E. / White, S. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.
Authors: Kielkopf, C.L. / Bremer, R.E. / White, S. / Szewczyk, J.W. / Turner, J.M. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
History
DepositionAug 24, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jan 15, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'
B: 5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4174
Polymers6,0902
Non-polymers1,3272
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.200, 34.200, 46.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Cell settingtrigonal
Space group name H-MP31

-
Components

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


Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-HP2 / HYDROXYPYRROLE-IMIDAZOLE-PYRROLE POLYAMIDE / IMIDAZOLE-PYRROLE-HYDROXYPYRROLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE


Mass: 663.727 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H41N11O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: CALCIUM ACETATE, TRIS, MPD, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM ACETATE11
2TRIS11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 mMduplex DNA1drop
21.3 mMpolyamide1drop
312 %1drop
435 mMCa acetate1drop
510 mMTris-HCl1drop
625 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→17 Å / Num. all: 2680 / Num. obs: 2680 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 42.3
Reflection shellResolution: 2.27→2.35 Å / Rmerge(I) obs: 0.204 / % possible all: 87
Reflection
*PLUS
Num. measured all: 7261
Reflection shell
*PLUS
% possible obs: 87 % / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.27→17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 134 5 %RANDOM
Rwork0.237 ---
obs0.237 2680 --
all-2680 --
Refinement stepCycle: LAST / Resolution: 2.27→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 106 30 540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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

+
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