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- PDB-7xdj: Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGAGCT)... -

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Basic information

Entry
Database: PDB / ID: 7xdj
TitleCrystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGAGCT) complex
Components
  • DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
  • DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
  • DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
  • THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
KeywordsDNA/ANTIBIOTIC / G:A mismatch / Single-strand DNA twist / mismatch binding antibiotic / DNA / DNA-ANTIBIOTIC complex
Function / homologyActinomycin D / Echinomycin / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesStreptomyces (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.435 Å
AuthorsChien, C.M. / Satange, R.B. / Hou, M.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2628-M-005-001-MY4 Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2311-B-005-007-MY3 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism.
Authors: Satange, R. / Kao, S.H. / Chien, C.M. / Chou, S.H. / Lin, C.C. / Neidle, S. / Hou, M.H.
History
DepositionMar 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
E: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
I: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
J: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
L: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
M: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
N: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
P: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
C: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
G: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
K: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
O: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
D: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
H: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,27730
Polymers25,70516
Non-polymers1,57314
Water61334
1
A: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
P: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
C: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8348
Polymers6,4264
Non-polymers4084
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
G: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
D: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7746
Polymers6,4264
Non-polymers3482
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
J: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
L: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
O: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8348
Polymers6,4264
Non-polymers4084
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
N: DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')
K: THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA
H: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8348
Polymers6,4264
Non-polymers4084
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.522, 132.522, 49.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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DNA chain , 2 types, 8 molecules AEIMBFJN

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


Mass: 2138.423 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
DNA (5'-D(P*AP*CP*GP*AP*GP*CP*(BRU))-3')


Mass: 2187.294 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide , 2 types, 8 molecules LPDHCGKO

#3: Protein/peptide
DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 809.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Source: (natural) Streptomyces (bacteria) / References: Echinomycin
#4: Protein/peptide
THR-DVA-PRO-SAR-MVA-PXZ-THR-DVA-PRO-SAR-MVA


Type: Polypeptide / Class: Antibiotic / Mass: 1291.446 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) Streptomyces (bacteria) / References: NOR: NOR00228, Actinomycin D

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Non-polymers , 4 types, 48 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H6N2O2
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: Echinomycin
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. ...THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.25 mM Oligonucleotide, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate, 3.5 mM Magnesium chloride, 1 mM Spermine tetrahydrochloride, 6 mM Cobalt chloride, 1% (v/v) 2- ...Details: 0.25 mM Oligonucleotide, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate, 3.5 mM Magnesium chloride, 1 mM Spermine tetrahydrochloride, 6 mM Cobalt chloride, 1% (v/v) 2-Methyl-2,4-pentanediol, 6% (v/v) PEG 200, Reservior PEG 200 (30%)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.91982 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91982 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 24192 / % possible obs: 99.8 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.027 / Rrim(I) all: 0.088 / Χ2: 1.208 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.44-2.539.70.75912160.8490.2520.8011.09798.1
2.53-2.6310.70.57912040.9260.1850.6081.055100
2.63-2.7511.40.512070.9490.1550.5231.026100
2.75-2.8911.60.32512440.9770.10.340.97100
2.89-3.0711.40.19311940.9950.060.2020.945100
3.07-3.3111.20.08812120.9990.0280.0920.957100
3.31-3.6411.10.07112070.9990.0230.0741.182100
3.64-4.1711.40.0712180.9980.0220.0731.286100
4.17-5.2511.30.06112100.9980.0190.0631.568100
5.25-3010.90.05812050.9990.0190.0612.01299.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DQ0

7dq0


Resolution: 2.435→24.835 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 2436 10.07 %
Rwork0.2008 21756 -
obs0.2043 24192 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.55 Å2 / Biso mean: 57.2815 Å2 / Biso min: 36.24 Å2
Refinement stepCycle: final / Resolution: 2.435→24.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms596 1156 438 34 2224
Biso mean--55.09 61.1 -
Num. residues----90
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4354-2.4850.33271390.299121994
2.485-2.5390.35771450.2854126899
2.539-2.5980.36871520.271319100
2.598-2.66290.28791360.29371244100
2.6629-2.73480.35821420.31371292100
2.7348-2.81520.46651440.2871278100
2.8152-2.90590.31231500.26521300100
2.9059-3.00960.29881400.24161298100
3.0096-3.12990.22571480.20841274100
3.1299-3.27210.21121440.17561272100
3.2721-3.44410.23161380.15591266100
3.4441-3.65930.29141420.18531272100
3.6593-3.94080.24231480.20821324100
3.9408-4.33550.19311420.17621262100
4.3355-4.95850.19161400.15281310100
4.9585-6.23090.16291420.17251270100
6.2309-24.830.21591440.21861288100
Refinement TLS params.Method: refined / Origin x: 5.3782 Å / Origin y: 25.8104 Å / Origin z: 11.6789 Å
111213212223313233
T0.3694 Å20.0356 Å2-0.0829 Å2-0.3021 Å20.0016 Å2--0.656 Å2
L0.8136 °20.704 °2-0.5747 °2-1.6557 °21.1958 °2--1.9811 °2
S0.0912 Å °0.1241 Å °-0.083 Å °0.2876 Å °-0.1501 Å °0.0745 Å °0.0812 Å °-0.1211 Å °0.0897 Å °
Refinement TLS groupSelection details: all

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