[English] 日本語
Yorodumi
- PDB-1a7z: CRYSTAL STRUCTURE OF ACTINOMYCIN Z3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a7z
TitleCRYSTAL STRUCTURE OF ACTINOMYCIN Z3
ComponentsACTINOMYCIN Z3
KeywordsANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / ANTICANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE
Function / homologyActinomycin Z3 / BENZENE / :
Function and homology information
Biological speciesSTREPTOMYCES FRADIAE (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 0.95 Å
AuthorsSchafer, M.
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACTINOMYCIN Z3
B: ACTINOMYCIN Z3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,27422
Polymers2,7122
Non-polymers1,56220
Water181
1
A: ACTINOMYCIN Z3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9819
Polymers1,3561
Non-polymers6258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACTINOMYCIN Z3
hetero molecules


  • defined by author
  • 2.29 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,29313
Polymers1,3561
Non-polymers93712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)14.803, 24.780, 65.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide ACTINOMYCIN Z3


Type: Polypeptide / Class: Antibiotic / Mass: 1355.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ACTINOMYCIN Z3 CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) STREPTOMYCES FRADIAE (bacteria) / References: NOR: NOR00237, Actinomycin Z3
#2: Chemical
ChemComp-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTINOMYCIN Z3 IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN Z3 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: PH 7
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Common name: benzene

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 22, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.95→32.45 Å / Num. obs: 15653 / % possible obs: 99.5 % / Redundancy: 7.06 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.17
Reflection shellResolution: 0.95→1.05 Å / Redundancy: 4.85 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.93 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 112696 / Rmerge(I) obs: 0.0602

-
Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: AB INITIO / Resolution: 0.95→32.45 Å / Num. parameters: 3024 / Num. restraintsaints: 5470 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: NO RESTRAINTS ON DISTANCES AND ANGLES
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.026
RfactorNum. reflection% reflectionSelection details
Rfree0.097 1568 10 %RANDOM
all0.081 15653 --
obs0.08 -99.4 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 286 / Occupancy sum non hydrogen: 307
Refinement stepCycle: LAST / Resolution: 0.95→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms186 0 120 1 307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.016
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_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.024
X-RAY DIFFRACTIONs_approx_iso_adps0.032
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.0797
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_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://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