[English] 日本語
Yorodumi
- PDB-6j0h: Crystal structure of Actinomycin D- d(TTGGCGAA) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j0h
TitleCrystal structure of Actinomycin D- d(TTGGCGAA) complex
Components
  • Actinomycin DDactinomycin
  • DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3')
KeywordsDNA/ANTIBIOTIC / Mismatch DNA / Actinomycin D / Drug-DNA complex / Base flip out / DNA kink / DNA-ANTIBIOTIC complex
Function / homologyActinomycin D / DNA
Function and homology information
Biological speciessynthetic construct (others)
Streptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsSatange, R.B. / Hou, M.H.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation.
Authors: Satange, R. / Chuang, C.Y. / Neidle, S. / Hou, M.H.
History
DepositionDec 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
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 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3')
B: Actinomycin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7493
Polymers3,7262
Non-polymers231
Water1,02757
1
A: DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3')
B: Actinomycin D
hetero molecules

A: DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3')
B: Actinomycin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4986
Polymers7,4524
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1/2,-z+1/41
Unit cell
Length a, b, c (Å)59.500, 59.500, 93.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-101-

NA

21A-242-

HOH

31B-102-

HOH

-
Components

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


Mass: 2466.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide Actinomycin D / Dactinomycin / Dactinomycin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1259.447 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (synth.) Streptomyces sp. (bacteria) / References: Actinomycin D
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.55 Å3/Da / Density % sol: 77.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5M Sodium malonate, 100mM lithium chloride, 10mM Manganese(II) chloride, 10mM MES (pH 6.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 13248 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 21.64 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.035 / Rrim(I) all: 0.121 / Χ2: 1.06 / Net I/σ(I): 8.5 / Num. measured all: 172564
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.52-1.5712.22.6812980.7620.792.7961.097100
1.57-1.6413.51.73912950.8990.4891.8071.094100
1.64-1.7114.11.05412990.9660.291.0941.074100
1.71-1.814.20.90113110.9630.2470.9351.075100
1.8-1.9114.10.55413130.9810.1530.5751.035100
1.91-2.0613.80.31113060.9920.0870.3241.079100
2.06-2.2713.70.19213210.9950.0540.21.086100
2.27-2.613.20.13113400.9960.0380.1361.042100
2.6-3.2712.80.06513530.9980.020.0681.011100
3.27-308.90.04214120.9990.0150.0450.98498

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→27.606 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1324 10.01 %
Rwork0.2091 11909 -
obs0.2098 13233 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.38 Å2 / Biso mean: 32.4932 Å2 / Biso min: 17.36 Å2
Refinement stepCycle: final / Resolution: 1.52→27.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90 167 1 58 316
Biso mean--40.39 45.83 -
Num. residues----19
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.043279
X-RAY DIFFRACTIONf_angle_d2.868419
X-RAY DIFFRACTIONf_chiral_restr0.27944
X-RAY DIFFRACTIONf_plane_restr0.01823
X-RAY DIFFRACTIONf_dihedral_angle_d36.59797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5199-1.58070.3021400.28871267140797
1.5807-1.65260.26451460.239113061452100
1.6526-1.73980.27971440.235712981442100
1.7398-1.84870.25981470.250913171464100
1.8487-1.99140.27811440.246613041448100
1.9914-2.19180.22821480.243713261474100
2.1918-2.50870.26851470.247213311478100
2.5087-3.160.2551510.234813521503100
3.16-27.61040.15391570.15891408156598

+
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