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- PDB-4m95: d(ATCCGTTATAACGGAT)complexed with Moloney Murine Leukemia virus r... -

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Basic information

Entry
Database: PDB / ID: 4m95
Titled(ATCCGTTATAACGGAT)complexed with Moloney Murine Leukemia virus reverse transcriptase catalytic fragment
Components
  • 5' d(ATCCGTTA) 3'
  • 5' d(TAACGGAT) 3'
  • Gag-Pol polyprotein
KeywordsTRANSFERASE/DNA / Protein-DNA complex / Reverse transcriptase / DNA binding / DNA sequence / 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
DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus isolate Shinnick
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsSingh, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition.
Authors: Singh, I. / Lian, Y. / Li, L. / Georgiadis, M.M.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Gag-Pol polyprotein
B: 5' d(ATCCGTTA) 3'
G: 5' d(TAACGGAT) 3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3866
Polymers34,2003
Non-polymers1863
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.329, 146.107, 46.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Gag-Pol polyprotein / Pr180gag-pol / Matrix protein p15 / MA / RNA-binding phosphoprotein p12 / pp12 / Capsid protein p30 ...Pr180gag-pol / Matrix protein p15 / MA / RNA-binding phosphoprotein p12 / pp12 / Capsid protein p30 / CA / Nucleocapsid protein p10 / NC-pol / Protease p14 / PR / Reverse transcriptase/ribonuclease H p80 / RT / Integrase p46 / IN


Mass: 29347.754 Da / Num. of mol.: 1 / Fragment: UNP residues 683-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus isolate Shinnick
Gene: gag-pol, Reverse transcriptase / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: P03355, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: DNA chain 5' d(ATCCGTTA) 3'


Mass: 2401.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Polydeoxyribonucleotide
#3: DNA chain 5' d(TAACGGAT) 3'


Mass: 2450.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Polydeoxyribonucleotide
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG 4000, 5mM Magnesium acetate, 50mM N-(2-acetamido)iminodiacetic acid, pH 6.5, vapor diffusion, hanging drop, temperature 293.15K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2013
RadiationMonochromator: Rosenbaum-Rock high resolution double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.72→26.7 Å / Num. all: 40829 / Num. obs: 40094 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 24.4

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→26.7 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.23 / σ(F): 0 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1949 5.02 %
Rwork0.211 --
obs0.212 38858 95.6 %
all-40829 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.31 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 34.98 Å2
Baniso -1Baniso -2Baniso -3
1-4.4364 Å20 Å2-0 Å2
2--1.2827 Å2-0 Å2
3----5.7191 Å2
Refinement stepCycle: LAST / Resolution: 1.72→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 325 12 187 2543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.04
X-RAY DIFFRACTIONf_angle_d0.954
X-RAY DIFFRACTIONf_dihedral_angle_d19.309
X-RAY DIFFRACTIONf_chiral_restr0.058
X-RAY DIFFRACTIONf_plane_restr0.005

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