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- PDB-8xp8: Crystal structure of d(ACGmCCGT/ACGGCGT) in complex with Echinomycin -

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Basic information

Entry
Database: PDB / ID: 8xp8
TitleCrystal structure of d(ACGmCCGT/ACGGCGT) in complex with Echinomycin
Components
  • DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3')
  • Echinomycin
KeywordsDNA/ANTIBIOTIC / DNA-ligand Complex / DNA / Antibiotic / DNA-ANTIBIOTIC complex
Function / homologyEchinomycin / : / 2-CARBOXYQUINOXALINE / DNA
Function and homology information
Biological speciesStreptomyces echinatus. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsHou, M.H. / Lin, S.M. / Neidle, H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.
Authors: Lin, S.M. / Huang, H.T. / Fang, P.J. / Chang, C.F. / Satange, R. / Chang, C.K. / Chou, S.H. / Neidle, S. / Hou, M.H.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: 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 1.2Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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*CP*GP*GP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3')
D: Echinomycin
E: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,73011
Polymers5,8694
Non-polymers8617
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.329, 46.329, 47.954
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

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DNA chain , 2 types, 2 molecules AB

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


Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3')


Mass: 2112.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide , 1 types, 2 molecules DE

#3: Protein/peptide Echinomycin


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 echinatus. (bacteria) / References: Echinomycin

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Non-polymers , 3 types, 54 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 4 / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20mM MES (pH 6), 5mM Spermine HCl, 1.2% PEG 200, 10mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 7315 / % possible obs: 98.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.64-1.710.70.1147210.99910.0380.121.033100
1.7-1.77110.1187350.99910.0380.1241.038100
1.77-1.85110.1027270.99810.0330.1081.061100
1.85-1.9411.10.0927360.99810.0290.0971.048100
1.94-2.0711.10.0817240.9970.9990.0260.0861.029100
2.07-2.2311.10.0737570.99810.0230.0761.072100
2.23-2.4511.10.0587270.99910.0180.0611.059100
2.45-2.810.90.0587350.99910.0190.0611.095100
2.8-3.5310.50.0537290.99910.0180.0560.95997.1
3.53-309.50.0487240.9980.9990.0170.0521.02692.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→16.66 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.41 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 716 9.89 %
Rwork0.2339 --
obs0.2348 7240 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→16.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 282 157 47 486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018
X-RAY DIFFRACTIONf_angle_d2.475
X-RAY DIFFRACTIONf_dihedral_angle_d32.4186
X-RAY DIFFRACTIONf_chiral_restr0.15186
X-RAY DIFFRACTIONf_plane_restr0.0142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.770.29421450.2721285X-RAY DIFFRACTION98
1.77-1.940.31431350.28991308X-RAY DIFFRACTION99
1.94-2.220.3491480.30161322X-RAY DIFFRACTION100
2.22-2.80.27021430.25541314X-RAY DIFFRACTION100
2.8-100.19611450.19611295X-RAY DIFFRACTION95
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)
15.33210.3096-0.13495.29390.08565.99950.03760.4163-0.4250.3952-0.2958-0.29080.89660.40220.24150.28630.00480.01310.2565-0.01050.295839.532111.905947.9784
23.05570.0682-0.36222.802-0.33322.47350.3730.5412-0.17250.5667-0.274-0.07950.5640.32790.05710.2665-0.0619-0.03090.32660.01340.282138.194914.077247.9596
30.0441-0.01980.01060.06190.00680.0047-0.00970.0121-0.01120.0097-0.00780.05970.0107-0.0113-0.00590.3074-0.1752-0.05160.0193-0.03650.132536.090916.074859.9244
40.11690.00930.10430.02180.00940.11990.01890.0493-0.005-0.01760.00880.03740.0096-0.0117-0.0020.2289-0.1155-0.02260.3190.06480.15541.744518.575150.7064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D'
2X-RAY DIFFRACTION2(chain 'A' and (resid 1 or resid 3 or resid 5 through 7)) or (chain 'B' and (resid 1 or resid 3 or resid 5 through 7))
3X-RAY DIFFRACTION3(chain 'B' and resid 2)
4X-RAY DIFFRACTION4(chain 'B' and resid 4)

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