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

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Basic information

Entry
Database: PDB / ID: 8xpb
TitleCrystal structure of d(ACGCCGT/ACGGCGT) in complex with Echinomycin
Components
  • DNA (5'-D(P*AP*CP*GP*CP*CP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3')
  • Echinomycin
KeywordsDNA/ANTIBIOTIC / complex / DNA / 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: 2 Å
AuthorsHou, M.H. / Huang, H.T. / Lin, S.M. / Neidle, S.
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*CP*CP*GP*T)-3')
D: Echinomycin
E: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,71611
Polymers5,8554
Non-polymers8617
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.317, 46.317, 47.971
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*CP*CP*GP*T)-3')


Mass: 2098.399 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, 27 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.: 20 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20mM MES (pH 6), 10mM Spermine HCl, 1% PEG 200, 10mM MnCl2

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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 MX300HE / Detector: CCD / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 4107 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.0710.40.4834100.9780.9940.1560.5081.089100
2.07-2.1510.80.3874030.980.9950.1230.4061.131100
2.15-2.2511.10.3043980.990.9980.0950.3191.141100
2.25-2.3711.10.1914100.9950.9990.0610.2011.147100
2.37-2.52110.1334060.99810.0420.141.179100
2.52-2.7111.10.1334010.9970.9990.0420.1391.091100
2.71-2.99110.0724160.99910.0230.0760.989100
2.99-3.4210.90.035404110.0110.0361.057100
3.42-4.3110.80.0434180.99910.0140.0450.906100
4.31-3010.20.026441110.0080.0270.96999.5

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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: 2→20.86 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 404 9.97 %
Rwork0.2107 --
obs0.2116 4052 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→20.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 281 157 20 458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d2.061
X-RAY DIFFRACTIONf_dihedral_angle_d32.355146
X-RAY DIFFRACTIONf_chiral_restr0.17372
X-RAY DIFFRACTIONf_plane_restr0.00938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.290.331290.26931213X-RAY DIFFRACTION99
2.29-2.880.27841360.27091206X-RAY DIFFRACTION99
2.89-100.17631390.17631229X-RAY DIFFRACTION98
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)
16.41590.6419-0.74664.9849-1.13834.11040.35120.7325-0.27930.4190.03160.22760.6611-0.5123-0.29190.3911-0.08030.01610.3407-0.05970.329433.867212.291946.141
25.5720.9937-1.93125.0113-0.09144.90290.76170.20780.19530.5332-0.2506-0.3128-0.05260.7474-0.51410.2659-0.0307-0.03990.46280.06140.363941.951816.956149.841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 7 )

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