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- PDB-3p1g: Crystal Structure of the Xenotropic Murine Leukemia Virus-Related... -

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Basic information

Entry
Database: PDB / ID: 3p1g
TitleCrystal Structure of the Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain
ComponentsXenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain
KeywordsTRANSCRIPTION / XMRV / RNase H / Reverse Transcriptase
Function / homology
Function and homology information


ribonuclease H / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...ribonuclease H / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / identical protein binding / membrane / plasma 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-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 / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesXenotropic MuLV-related virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsKirby, K.A. / Sarafianos, S.G.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2012
Title: Structural and Inhibition Studies of the RNase H Function of Xenotropic Murine Leukemia Virus-Related Virus Reverse Transcriptase.
Authors: Kirby, K.A. / Marchand, B. / Ong, Y.T. / Ndongwe, T.P. / Hachiya, A. / Michailidis, E. / Leslie, M.D. / Sietsema, D.V. / Fetterly, T.L. / Dorst, C.A. / Singh, K. / Wang, Z. / Parniak, M.A. / Sarafianos, S.G.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Apr 4, 2012Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9932
Polymers17,9681
Non-polymers241
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.530, 37.530, 100.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain


Mass: 17968.305 Da / Num. of mol.: 1 / Mutation: 595-605 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenotropic MuLV-related virus / Production host: Escherichia coli (E. coli) / References: UniProt: D0UFA6, UniProt: A1Z651*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: PEG 1500, Magnesium Chloride, Sodium Citrate, pH 4.7, Vapor Diffusion, Hanging Drop, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→37.53 Å / Num. obs: 22272 / % possible obs: 99.9 % / Redundancy: 6.77 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.553.660.7712.1199.3
1.55-1.625.090.752.41100
1.62-1.697.110.66531100
1.69-1.787.410.3183.61100
1.78-1.897.420.2664.31100
1.89-2.047.270.2365.91100
2.04-2.247.270.1787.21100
2.24-2.567.460.1448.51100
2.56-3.237.570.09511.81100
3.23-37.537.360.0524.2199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→37.53 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.15 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 1122 5.11 %
Rwork0.161 --
obs0.163 21970 98.8 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 1 162 1369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061301
X-RAY DIFFRACTIONf_angle_d0.9951778
X-RAY DIFFRACTIONf_dihedral_angle_d12.1505
X-RAY DIFFRACTIONf_chiral_restr0.064200
X-RAY DIFFRACTIONf_plane_restr0.004236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56840.24811470.21452497X-RAY DIFFRACTION95
1.5684-1.65110.21281450.17832611X-RAY DIFFRACTION99
1.6511-1.75450.29321260.20482587X-RAY DIFFRACTION99
1.7545-1.890.23021480.18532593X-RAY DIFFRACTION99
1.89-2.08020.19431240.15692648X-RAY DIFFRACTION99
2.0802-2.38110.18071560.15512612X-RAY DIFFRACTION100
2.3811-2.99980.19071340.15842637X-RAY DIFFRACTION100
2.9998-37.54170.15311420.15262663X-RAY DIFFRACTION100

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