[English] 日本語
Yorodumi
- PDB-1qfi: SYNTHESIS AND STRUCTURE OF PROLINE RING MODIFIED ACTINOMYCINS OF ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qfi
TitleSYNTHESIS AND STRUCTURE OF PROLINE RING MODIFIED ACTINOMYCINS OF X TYPE
ComponentsACTINOMYCIN X2
KeywordsANTIBIOTIC / ACTINOMYCIN / ANTICANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE
Function / homologyActinomycin X2 / ETHYL ACETATE / METHANOL / :
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 0.91 Å
AuthorsLifferth, A. / Bahner, I. / Lackner, H. / Schaefer, M.
CitationJournal: Z.Naturforsch. / Year: 1999
Title: Synthesis and Structure of Proline Ring Modified Actinomycins of the X-Type
Authors: Lifferth, A. / Bahner, I. / Lackner, H. / Schaefer, M.
History
DepositionApr 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: 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 1.5Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software / Item: _software.name
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
Revision 3.1Oct 9, 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: ACTINOMYCIN X2
B: ACTINOMYCIN X2
C: ACTINOMYCIN X2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,69315
Polymers3,9163
Non-polymers77712
Water00
1
A: ACTINOMYCIN X2
hetero molecules


  • defined by author
  • 1.78 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,7787
Polymers1,3051
Non-polymers4736
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACTINOMYCIN X2


Theoretical massNumber of molelcules
Total (without water)1,3051
Polymers1,3051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ACTINOMYCIN X2
hetero molecules


  • defined by author
  • 1.61 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,6107
Polymers1,3051
Non-polymers3046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)15.594, 16.009, 25.322
Angle α, β, γ (deg.)86.23, 85.16, 69.65
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide ACTINOMYCIN X2 / ACTINOMYCIN V


Type: Polypeptide / Class: Antibiotic / Mass: 1305.430 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: ACTINOMYCIN X2 CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (synth.) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00232, Actinomycin X2
#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.: 5 / Source method: obtained synthetically / Formula: CH4O
Compound detailsACTINOMYCIN X2 IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN X2 IS ...ACTINOMYCIN X2 IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN X2 IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.12 Å3/Da / Density % sol: 20.37 %
Crystal growpH: 5 / Details: PH 5.00

-
Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54178
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 0.91→25.15 Å / Num. obs: 15506 / % possible obs: 94.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.047 / Rsym value: 0.015 / Net I/σ(I): 43.4
Reflection shellResolution: 0.91→1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 14.7 / Rsym value: 0.066 / % possible all: 82.9

-
Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.91→25.15 Å / Num. parameters: 2994 / Num. restraintsaints: 3955 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.065 15506 -
obs--94.2 %
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 307.6 / Occupancy sum non hydrogen: 310.8
Refinement stepCycle: LAST / Resolution: 0.91→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms273 0 52 0 325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.027
X-RAY DIFFRACTIONs_from_restr_planes0.124
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_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.056

+
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