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- PDB-1nnd: Arginine 116 is Essential for Nucleic Acid Recognition by the Fin... -

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Basic information

Entry
Database: PDB / ID: 1nnd
TitleArginine 116 is Essential for Nucleic Acid Recognition by the Fingers Domain of Moloney Murine Leukemia Virus Reverse Transcriptase
ComponentsReverse Transcriptase
KeywordsTRANSFERASE / Nucleic Acid Binding / MMLV Reverse Transcriptase
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / 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. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase domain superfamily / Ribonuclease H 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
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCrowther, R.L. / Remeta, D.P. / Minetti, C.A. / Das, D. / Montano, S.P. / Georgiadis, M.M.
CitationJournal: Proteins / Year: 2004
Title: Structural and energetic characterization of nucleic acid-binding to the fingers domain of Moloney murine leukemia virus reverse transcriptase
Authors: Crowther, R.L. / Remeta, D.P. / Minetti, C.A. / Das, D. / Montano, S.P. / Georgiadis, M.M.
History
DepositionJan 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reverse Transcriptase


Theoretical massNumber of molelcules
Total (without water)28,8481
Polymers28,8481
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.795, 116.652, 61.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein Reverse Transcriptase / E.C.2.7.7.49 / MMLV RT


Mass: 28848.170 Da / Num. of mol.: 1 / Fragment: MMLV Reverse Transcriptase / Mutation: R116A
Source method: isolated from a genetically manipulated source
Details: part of Pol polyprotein / Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: Reverse Transcriptase / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.33 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, Magnesium Chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.55 mMprotein1drop
21.1 mM5'-d(CATGCATG)-3'1drop
312-18 %PEG4001drop
450 mMHEPES1droppH7.0
55 mM1dropMgCl2
62-6 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2000 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13028 / Num. obs: 12449 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.38 Å / % possible all: 83.9
Reflection
*PLUS
Num. obs: 12471 / % possible obs: 95.8 % / Num. measured all: 58875 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.35 Å / % possible obs: 83.9 % / Rmerge(I) obs: 0.13

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAI MOLECULE A

1qai


Resolution: 2.3→32.84 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1219 9.8 %RANDOM
Rwork0.203 ---
all0.21 13028 --
obs0.21 12449 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9656 Å2 / ksol: 0.342102 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.98 Å20 Å20 Å2
2--8.02 Å20 Å2
3----3.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 135 2136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it3.51.5
X-RAY DIFFRACTIONc_mcangle_it4.872
X-RAY DIFFRACTIONc_scbond_it5.182
X-RAY DIFFRACTIONc_scangle_it6.62.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 173 9.5 %
Rwork0.194 1648 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.253
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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