[English] 日本語
Yorodumi
- PDB-1mnv: Actinomycin D binding to ATGCTGCAT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mnv
TitleActinomycin D binding to ATGCTGCAT
Components
  • 5'-D(*AP*TP*GP*CP*TP*GP*CP*AP*T)-3'
  • ACTINOMYCIN D
KeywordsDNA/ANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / ANTIBIOTIC / ANTI CANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE / DNA-ANTIBIOTIC COMPLEX
Function / homologyActinomycin D / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsHou, M.-H. / Robinson, H. / Gao, Y.-G. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Crystal Structure of Actinomycin D Bound to the Ctg Triplet Repeat Sequences Linked to Neurological Diseases
Authors: Hou, M.-H. / Robinson, H. / Gao, Y.-G. / Wang, A.H.-J.
History
DepositionSep 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,0454
Polymers8,0454
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-6.3 kcal/mol
Surface area4030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.240, 47.240, 69.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

-
Components

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


Mass: 2730.810 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Protein/peptide ACTINOMYCIN D / DACTINOMYCIN


Type: Polypeptide / Class: Antibiotic / Mass: 1291.446 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (gene. exp.) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, Actinomycin D
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growpH: 6
Details: SODIUM-CACODYLATE BUFFER (PH 6.0), 10 MM BACL2, 3 MM SPERMINE, 4 % MPD SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 323K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium-cacodylate buffer11
2BaCl211
3spermine11
4MPD11
5BaCl212
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.3 mMDNA single strand1drop
21.3 mMActD1drop
340 mMsodium cacodylate1droppH6.0
410 mM1dropBaCl2
53 mMspermine1drop
64 %1drop
750 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.953
RadiationMonochromator: 3X3 MOSAIC CCD DETECTOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.6→80 Å / Num. obs: 25064 / % possible obs: 96.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 29.1
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 14.4 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 2650
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 99 %

-
Processing

Software
NameClassification
CNSrefinement
X-PLORrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 5
RfactorNum. reflection% reflectionSelection details
Rfree0.295 120 -RANDOM
Rwork0.233 ---
obs0.233 2650 95 %-
Displacement parametersBiso mean: 5.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms180 362 0 65 607
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.295 -5 %
Rwork0.233 2650 -
obs--95 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.018
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg3.1

+
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