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- PDB-7x9f: Crystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGCGCT)... -

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Basic information

Entry
Database: PDB / ID: 7x9f
TitleCrystal structure of actinomycin D-echinomycin-d(AGCGCGT/ACGCGCT) complex
Components
  • DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-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-PXF-THR-DVA-PRO-SAR-MVA
KeywordsDNA/ANTIBIOTIC / G:C canonical DNA / Single-strand DNA twist / four-way junction / Echinomycin / Actinomycin D / 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: 2.96 Å
AuthorsKao, S.H. / 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 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')
O: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
G: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
H: THR-DVA-PRO-SAR-MVA-PXF-THR-DVA-PRO-SAR-MVA
D: DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')
B: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
A: THR-DVA-PRO-SAR-MVA-PXF-THR-DVA-PRO-SAR-MVA
C: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,36213
Polymers12,6118
Non-polymers7525
Water1267
1
F: DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')
O: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
G: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
H: THR-DVA-PRO-SAR-MVA-PXF-THR-DVA-PRO-SAR-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7097
Polymers6,3054
Non-polymers4033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')
B: DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')
A: THR-DVA-PRO-SAR-MVA-PXF-THR-DVA-PRO-SAR-MVA
C: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6546
Polymers6,3054
Non-polymers3482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.917, 87.917, 47.551
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11O-101-

MN

21D-101-

HOH

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Components

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DNA chain , 2 types, 4 molecules FDOB

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


Mass: 2098.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*CP*GP*CP*GP*T)-3')


Mass: 2138.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide , 2 types, 4 molecules GCHA

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


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 809.008 Da / Num. of mol.: 2 / 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-PXF-THR-DVA-PRO-SAR-MVA / Dactinomycin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1259.447 Da / Num. of mol.: 2 / 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: Actinomycin D

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Non-polymers , 3 types, 12 molecules

#5: Chemical
ChemComp-QUI / 2-CARBOXYQUINOXALINE


Mass: 174.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H6N2O2
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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.
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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 mM MES buffer (pH 6.0), 5 mM Spermine tetrahydrochloride, 2% PEG200, 3 mM Manganese chloride, 0.25 mM Oligonucleotides, 0.25 mM echinomycin, 0.125 mM actinomycin D

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→30 Å / Num. obs: 4205 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 53.86 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.034 / Rrim(I) all: 0.094 / Χ2: 1.196 / Net I/σ(I): 9.2 / Num. measured all: 31951
Reflection shellResolution: 2.96→3.07 Å / Redundancy: 8 % / Rmerge(I) obs: 0.75 / Num. unique obs: 475 / CC1/2: 0.999 / Rpim(I) all: 0.012 / Rrim(I) all: 0.032 / Χ2: 1.035 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DQ0

7dq0


Resolution: 2.96→27.8 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 419 10.04 %
Rwork0.212 3755 -
obs0.218 4174 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.3 Å2 / Biso mean: 76.81 Å2 / Biso min: 35.23 Å2
Refinement stepCycle: final / Resolution: 2.96→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms286 574 49 7 916
Biso mean--58.12 48.65 -
Num. residues----66
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9601-3.38780.32721350.25261198133398
3.3878-4.26570.27291360.225112281364100
4.2657-27.80.24031480.190913291477100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.1551-4.10448.25696.8528-7.75282.03270.1022-1.265-0.26490.6991.27122.2963-0.339-0.2271-0.07861.24730.1643-0.18081.03130.06250.584532.02138.990210.0574
26.19454.03094.02774.55295.20546.13740.1559-0.168-0.62390.65720.7285-0.1607-0.4460.7135-0.97590.7675-0.0136-0.11221.05590.10520.470837.8281.6218.9744
37.5382.0922-3.04832.788-3.91255.4989-0.1040.49440.11721.04141.3255-0.6074-0.59861.93120.21431.16670.08560.02250.8205-0.20220.398639.03989.991417.3452
48.53491.1051-7.46677.38763.63679.46050.55970.63270.88480.9443-1.2653-0.7879-0.1494-0.201-0.43030.8005-0.3127-0.22890.82440.36740.676734.86149.80340.3886
51.91572.74050.63334.5051-0.30412.33291.67881.43062.27780.88010.14442.7886-1.2797-0.9955-1.77430.7625-0.00950.2030.80420.06420.98913.3892-11.391315.9344
67.34654.7875-3.97087.1504-6.1849.7389-0.6925-0.0888-0.94370.4756-1.074-0.40210.4223-0.33920.81940.7903-0.04390.10531.04080.12090.649118.0089-18.843320.0233
77.07770.23891.86874.161-0.29020.52440.5711-1.40640.53931.6441-0.55450.67220.223-0.265-0.11660.7368-0.6950.23340.89870.40680.386123.8268-10.003216.9438
84.0001-1.55885.63418.1139-3.15498.0605-0.3472-2.3339-0.60270.7863-0.09430.4173-0.6165-0.40740.92320.9969-0.04230.46630.72960.00190.87847.864-14.593925.3349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'F' AND (RESID -5 THROUGH 1 )F0
2X-RAY DIFFRACTION2CHAIN 'O' AND (RESID -5 THROUGH 1 )O0
3X-RAY DIFFRACTION3CHAIN 'G' AND (RESID 2 THROUGH 6 )G0
4X-RAY DIFFRACTION4CHAIN 'H' AND (RESID 1 THROUGH 9 )H0
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID -5 THROUGH 1 )D0
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID -5 THROUGH 1 )B0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 1 THROUGH 9 )A0
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 2 THROUGH 6 )C0

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