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- PDB-8dwm: Host-guest complex of bleomycin A2 fully bound to CTTAGTTATAACTAAG -

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Basic information

Entry
Database: PDB / ID: 8dwm
TitleHost-guest complex of bleomycin A2 fully bound to CTTAGTTATAACTAAG
Components
  • DNA (5'-D(*CP*TP*TP*AP*GP*TP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')
  • reverse transcriptase
KeywordsDNA BINDING PROTEIN/DNA / host-guest complex / Moloney murine leukemia virus reverse transcriptase / bleomycin A2 / DNA structure / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination ...host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / : / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
COBALT (III) ION / BLEOMYCIN A2 / DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.99 Å
AuthorsGeorgiadis, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
American Cancer Society United States
CitationJournal: Bioorg.Med.Chem. / Year: 2023
Title: Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites.
Authors: Goodwin, K.D. / Lewis, M.A. / Long, E.C. / Georgiadis, M.M.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,3505
Polymers34,8753
Non-polymers1,4752
Water543
1
A: reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*AP*GP*TP*TP*A)-3')
G: DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)72,70110
Polymers69,7506
Non-polymers2,9514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)52.808, 144.292, 49.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein reverse transcriptase


Mass: 30023.531 Da / Num. of mol.: 1 / Fragment: N-terminal fragment (UNP residues 683-937)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pro-pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UN00

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DNA chain , 2 types, 2 molecules BG

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


Mass: 2416.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')


Mass: 2434.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-BLM / BLEOMYCIN A2 / N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE


Mass: 1416.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H85N17O21S3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals of the host-guest complex were grown in 5 mM magnesium acetate, 0.05 M ADA pH 6.5, 9% PEG4000. To obtain complexes with BLM, crystals were soaked in well solutions containing 0.1 mM ...Details: Crystals of the host-guest complex were grown in 5 mM magnesium acetate, 0.05 M ADA pH 6.5, 9% PEG4000. To obtain complexes with BLM, crystals were soaked in well solutions containing 0.1 mM BLM followed by stabilization in 9% PEG4000, 5 mM magnesium acetate, 100 mM HEPES, pH 8.0, 20% ethylene glycol, 0.25 mM BLM until unit cell changes correlating with binding of BLM were detected.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 7774 / % possible obs: 94.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.97 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.056 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.113.20.2875421.086167.7
3.11-3.233.30.2196811.09186.9
3.23-3.383.70.1827681.063195.3
3.38-3.5640.1638081.073199.8
3.56-3.7840.1318021.071199.9
3.78-4.073.90.1078091.058199.3
4.07-4.483.90.0798071.069199.4
4.48-5.133.80.0668161.022198.9
5.13-6.463.80.0638401.098199.9
6.46-5040.0429010.967198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.20.1_4487refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZTW

1ztw


Resolution: 2.99→49.88 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2967 354 4.59 %
Rwork0.2247 7354 -
obs0.2282 7708 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.71 Å2 / Biso mean: 52.6544 Å2 / Biso min: 12.2 Å2
Refinement stepCycle: final / Resolution: 2.99→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 304 178 3 2474
Biso mean--90.78 38.11 -
Num. residues----263
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 (%)
2.99-3.420.3056860.27072146223284
3.42-4.310.31481330.2232535266899
4.31-49.880.28061350.20922673280899

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