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- PDB-2r2s: Co(III)bleomycinB2 bound to d(ATTAGTTATAACTAAT) complexed with MM... -

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Basic information

Entry
Database: PDB / ID: 2r2s
TitleCo(III)bleomycinB2 bound to d(ATTAGTTATAACTAAT) complexed with MMLV RT catalytic fragment
Components
  • DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DT)-3')
  • DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3')
  • Reverse transcriptase
Keywordstransferase/DNA / bleomycin / drug-DNA complex / protein-DNA complex / MMLV RT / DNA integration / DNA recombination / Endonuclease / Multifunctional enzyme / Nuclease / Nucleotidyltransferase / RNA-directed DNA polymerase / Transferase / transferase-DNA COMPLEX
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / 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 / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALT (III) ION / BLEOMYCIN B2 / DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsGoodwin, K.D. / Lewis, M.A. / Long, E.C. / Georgiadis, M.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding.
Authors: Goodwin, K.D. / Lewis, M.A. / Long, E.C. / Georgiadis, M.M.
History
DepositionAug 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DT)-3')
G: DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3')
A: Reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9575
Polymers33,4713
Non-polymers1,4852
Water90150
1
B: DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DT)-3')
G: DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3')
A: Reverse transcriptase
hetero molecules

B: DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DT)-3')
G: DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3')
A: Reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,91410
Polymers66,9436
Non-polymers2,9714
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)52.304, 144.508, 50.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is equivalent to 15 base pairs of DNA intercalated by two molecules of BLM with one molecule of MMLV RT bound on each end of the DNA. Symmetry is generated from the asymmetric unit by the operations: x, y, z and 2-x, 1-y, z.

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Components

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DNA chain , 2 types, 2 molecules BG

#1: DNA chain DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DT)-3')


Mass: 2127.433 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3')


Mass: 2409.630 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein Reverse transcriptase /


Mass: 28934.287 Da / Num. of mol.: 1 / Fragment: residues 144-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase

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Non-polymers , 3 types, 52 molecules

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


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-BLB / BLEOMYCIN B2


Mass: 1426.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H85N20O21S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 4000, MgCl2, pH 6.5, vapor diffusion, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2MgCl211
3PEG 400012
4MgCl212

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.039341 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2006
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039341 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9748 / % possible obs: 96.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Χ2: 1.032 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.92.70.3687970.76482
2.9-3.023.20.3369150.90193
3.02-3.153.60.2459551.0797.5
3.15-3.324.20.1849801.07799.4
3.32-3.534.50.1579821.058100
3.53-3.84.80.12810021.06399.9
3.8-4.184.60.0949931.03699.8
4.18-4.794.50.07410211.0299.6
4.79-6.034.20.06110181.01999.3
6.03-504.30.04310851.10397.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
RefinementResolution: 2.8→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.308 477 4.8 %
Rwork0.228 --
obs-9110 91.8 %
Solvent computationBsol: 23.688 Å2
Displacement parametersBiso mean: 42.661 Å2
Baniso -1Baniso -2Baniso -3
1--6.581 Å20 Å20 Å2
2--10.192 Å20 Å2
3----3.611 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 304 99 50 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.35
X-RAY DIFFRACTIONc_mcbond_it1.5661.5
X-RAY DIFFRACTIONc_scbond_it2.0592
X-RAY DIFFRACTIONc_mcangle_it2.7932
X-RAY DIFFRACTIONc_scangle_it3.4162.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION4blb.parblb.top
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

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