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- PDB-2r2r: d(ATTAGTTATAACTAAT) complexed with MMLV RT catalytic fragment -

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Basic information

Entry
Database: PDB / ID: 2r2r
Titled(ATTAGTTATAACTAAT) complexed with MMLV RT catalytic fragment
Components
  • DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DTP*DA)-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 / Aspartyl protease / DNA recombination / Endonuclease / Multifunctional enzyme / Nuclease / Nucleotidyltransferase / RNA-directed DNA polymerase / transferase-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Alpha-Beta Plaits / Roll ...Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Antitermination protein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*DTP*DA)-3')
G: DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3')
A: Reverse transcriptase


Theoretical massNumber of molelcules
Total (without water)33,7853
Polymers33,7853
Non-polymers00
Water2,918162
1
B: DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DTP*DA)-3')
G: DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3')
A: Reverse transcriptase

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


Theoretical massNumber of molelcules
Total (without water)67,5696
Polymers67,5696
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)55.662, 144.479, 46.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a 16mer of DNA bound on each end by one molecule of MMLV RT generated from the 8mer and 1 RT molecule in the asymmetric unit by the operations: x, y, z and 2-x, 1-y, z.

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Components

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


Mass: 2440.640 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
#3: Protein Reverse transcriptase / RT


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
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: 1.068828 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2007
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.068828 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 21887 / % possible obs: 95.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Χ2: 1.046 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.182.10.44417031.04676.4
2.18-2.262.80.37620541.08491.4
2.26-2.373.30.31721681.09596.8
2.37-2.493.60.24122241.09498.6
2.49-2.6540.222561.07899.8
2.65-2.854.10.15222451.074100
2.85-3.144.20.09922901.04699.7
3.14-3.594.20.072278199.3
3.59-4.524.30.05322990.98498.8
4.52-504.40.03323701.00995.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
RefinementResolution: 2.1→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 1022 4.5 %
Rwork0.238 --
obs-20890 91.5 %
Solvent computationBsol: 45.732 Å2
Displacement parametersBiso mean: 42.837 Å2
Baniso -1Baniso -2Baniso -3
1--5.124 Å20 Å20 Å2
2--3.957 Å20 Å2
3---1.167 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 325 0 162 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.263
X-RAY DIFFRACTIONc_mcbond_it1.7221.5
X-RAY DIFFRACTIONc_scbond_it2.0792
X-RAY DIFFRACTIONc_mcangle_it2.9442
X-RAY DIFFRACTIONc_scangle_it3.1972.5
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:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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