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- PDB-3fsi: Crystal structure of a trypanocidal 4,4'-Bis(imidazolinylamino)di... -

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Basic information

Entry
Database: PDB / ID: 3fsi
TitleCrystal structure of a trypanocidal 4,4'-Bis(imidazolinylamino)diphenylamine bound to DNA
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 domain
KeywordsTRANSFERASE/DNA / TRANSFERASE/DNA MMLV RT / PROTEIN-DNA COMPLEX / DRUG-DNA COMPLEX / CD27 / antitrypanosomal / DNA integration / DNA recombination / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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 / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
ACETATE ION / Chem-MWB / DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsGlass, L.S. / Georgiadis, M.M. / Goodwin, K.D.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA.
Authors: Glass, L.S. / Nguyen, B. / Goodwin, K.D. / Dardonville, C. / Wilson, W.D. / Long, E.C. / Georgiadis, M.M.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
A: Reverse transcriptase domain
G: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
B: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4169
Polymers33,7863
Non-polymers6316
Water4,107228
1
A: Reverse transcriptase domain
G: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
B: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)68,83218
Polymers67,5716
Non-polymers1,26112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)53.743, 145.592, 46.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsTwo protein molecules joined by a 16mer-bp double strand of DNA, with CD27 bound to both 5'-AATT sites. One asymmetric unit retains one half of the 16mer-bp, one protein and one bound ligand.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Reverse transcriptase domain / / RT


Mass: 28934.287 Da / Num. of mol.: 1
Fragment: Reverse transcriptase domain: UNP residues 144-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: MoMLV, pol / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P03355, RNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules GB

#2: 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
#3: 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

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Non-polymers , 3 types, 234 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MWB / N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine / CD27 / CD27


Mass: 335.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N7 / Comment: anticancer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
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
4PEG 400012
5Magnesium acetate12
6ADA12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008001 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2006
Details: Rosenbaum-Rock vertical focusing mirror, LN2 cooled first crystal, sagital focusing 2nd crystal
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008001 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 35935 / % possible obs: 95 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.045 / Χ2: 1.037 / Net I/σ(I): 24.677
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.813.90.35535100.99194.6
1.81-1.894.70.29135701.077195.4
1.89-1.974.80.19135611.172195.7
1.97-2.074.80.12335951.098196.4
2.07-2.24.80.08836151.083197
2.2-2.384.80.06736381.082196.9
2.38-2.614.80.05636540.989197
2.61-2.994.70.05236650.973196.3
2.99-3.774.40.03835380.897192.3
3.77-504.70.0335890.983188.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZTW

1ztw


Resolution: 1.75→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.838 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.254 1727 4.6 %
Rwork0.231 --
obs-34619 91.6 %
Solvent computationBsol: 52.54 Å2
Displacement parametersBiso max: 69.37 Å2 / Biso mean: 32.116 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1--5.807 Å20 Å20 Å2
2--3.138 Å20 Å2
3---2.669 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 325 45 228 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.263
X-RAY DIFFRACTIONc_mcbond_it1.3691.5
X-RAY DIFFRACTIONc_scbond_it1.8662
X-RAY DIFFRACTIONc_mcangle_it2.1772
X-RAY DIFFRACTIONc_scangle_it2.8492.5
LS refinement shellResolution: 1.75→1.8 Å / Num. reflection obs: 3510
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 DIFFRACTION4act.paract.top
X-RAY DIFFRACTION5cdx.parcdx.top

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