[English] 日本語
Yorodumi
- PDB-1a7y: CRYSTAL STRUCTURE OF ACTINOMYCIN D -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a7y
TitleCRYSTAL STRUCTURE OF ACTINOMYCIN D
ComponentsACTINOMYCIN D
KeywordsANTIBIOTIC / ACTINOMYCIN / ANTITUMOR / ANTICANCER / CHROMOPHORE / DEPSIPEPTIDE
Function / homologyActinomycin D / ETHYL ACETATE / METHANOL / :
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 0.94 Å
AuthorsSchafer, M. / Sheldrick, G.M. / Bahner, I. / Lackner, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 1998
Title: Crystal Structures of Actinomycin D and Actinomycin Z3.
Authors: Schafer, M. / Sheldrick, G.M. / Bahner, I. / Lackner, H.
History
DepositionMar 19, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: 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 1.5Mar 7, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_validate_polymer_linkage
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.6Nov 13, 2019Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_id_ASTM / _citation.journal_id_CSD ..._citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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 / _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: ACTINOMYCIN D
B: ACTINOMYCIN D
C: ACTINOMYCIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,42711
Polymers3,7783
Non-polymers6498
Water00
1
A: ACTINOMYCIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6125
Polymers1,2591
Non-polymers3524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)1,2591
Polymers1,2591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ACTINOMYCIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5565
Polymers1,2591
Non-polymers2964
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)15.737, 15.887, 25.156
Angle α, β, γ (deg.)85.93, 86.19, 69.86
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide ACTINOMYCIN D / DACTINOMYCIN


Type: Polypeptide / Class: Antibiotic / Mass: 1259.447 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, Actinomycin D
#2: Chemical
ChemComp-EEE / ETHYL ACETATE


Mass: 88.105 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 18 %
Crystal growpH: 5 / Details: PH 5.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Common name: ethyl acetate/methanol

-
Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 3, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.94→999 Å / Num. obs: 14126 / % possible obs: 95.1 % / Redundancy: 4.38 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 25.9
Reflection shellResolution: 0.94→1.05 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 11.9 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 95014

-
Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: AB INITIO / Highest resolution: 0.94 Å / Num. parameters: 2875 / Num. restraintsaints: 3689 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: NO RESTRAINTS ON DISTANCES AND ANGLES
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.039
RfactorNum. reflection% reflectionSelection details
Rfree0.068 1401 9.9 %RANDOM
all0.057 14126 --
obs0.058 -95.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 318 / Occupancy sum non hydrogen: 314
Refinement stepCycle: LAST / Highest resolution: 0.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms270 0 44 0 314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.024
X-RAY DIFFRACTIONs_from_restr_planes0.163
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.575
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d

+
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