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- PDB-2fjv: RT29 Bound to D(CTTAATTCGAATTAAG) in complex with MMLV RT Catalyt... -

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Basic information

Entry
Database: PDB / ID: 2fjv
TitleRT29 Bound to D(CTTAATTCGAATTAAG) in complex with MMLV RT Catalytic Fragment
Components
  • 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
  • 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
  • Reverse transcriptase
KeywordsTRANSFERASE/DNA / MMLV RT / PROTEIN-DNA COMPLEX / water-mediated interaction / DRUG-DNA COMPLEX / RT29 / benzamidazole / 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 / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HXL / DNA / Antitermination protein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGoodwin, K.D. / Georgiadis, M.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine.
Authors: Goodwin, K.D. / Lewis, M.A. / Tanious, F.A. / Tidwell, R.R. / Wilson, W.D. / Georgiadis, M.M. / Long, E.C.
History
DepositionJan 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
G: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
A: Reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1564
Polymers33,7863
Non-polymers3701
Water3,999222
1
B: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
G: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
A: Reverse transcriptase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)68,3128
Polymers67,5716
Non-polymers7412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)54.552, 145.65, 46.838
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'


Mass: 2376.591 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'


Mass: 2474.667 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Reverse transcriptase / RT


Mass: 28934.287 Da / Num. of mol.: 1 / Fragment: RT catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase
#4: Chemical ChemComp-HXL / 2-(4-(4-CARBAMIMIDOYLPHENOXY)PHENYL)-1H-BENZO[D]IMIDAZOLE-6-CARBOXIMIDAMIDE / 2-(4-{4-[AMINO(IMINO)METHYL]PHENOXY}PHENYL)-1H-BENZIMIDAZOLE-5-CARBOXIMIDAMIDE


Mass: 370.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, MAGNESIUM ACETATE, ADA PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2MAGNESIUM ACETATE11
3ADA11
4H2O11
5PEG 400012
6MAGNESIUM ACETATE12
7ADA12
8H2O12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 22, 2005
RadiationMonochromator: OSMIC CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 23358 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.05→2.12 Å / % possible all: 94.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.28 1093 random
Rwork0.228 --
all0.29 --
obs0.228 22534 -
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 325 28 222 2616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.32

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