+Open data
-Basic information
Entry | Database: PDB / ID: 1mu2 | ||||||
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Title | CRYSTAL STRUCTURE OF HIV-2 REVERSE TRANSCRIPTASE | ||||||
Components | (HIV-2 RT) x 2 | ||||||
Keywords | TRANSFERASE / HIV-2 REVERSE TRANSCRIPTASE / AIDS / POLYMERASE / DRUG DESIGN | ||||||
Function / homology | Function and homology information HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression ...HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ren, J. / Bird, L.E. / Chamberlain, P.P. / Stewart-Jones, G.B. / Stuart, D.I. / Stammers, D.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Structure of HIV-2 reverse transcriptase at 2.35-A resolution and the mechanism of resistance to non-nucleoside inhibitors Authors: Ren, J. / Bird, L.E. / Chamberlain, P.P. / Stewart-Jones, G.B. / Stuart, D.I. / Stammers, D.K. #1: Journal: To be Published Title: Cloning, Expression, Purification, and Crystallisation of HIV-2 Reverse Transcriptase Authors: Bird, L.E. / Chamberlain, P.P. / Stewart-Jones, G.B. / Ren, J. / Stuart, D.I. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mu2.cif.gz | 217 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mu2.ent.gz | 170.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mu2_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 1mu2_full_validation.pdf.gz | 491.9 KB | Display | |
Data in XML | 1mu2_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 1mu2_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/1mu2 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/1mu2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64169.555 Da / Num. of mol.: 1 / Mutation: R286S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Strain: pROD / Gene: POL / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P04584, RNA-directed DNA polymerase | ||||
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#2: Protein | Mass: 50181.730 Da / Num. of mol.: 1 / Fragment: residues 6-431 / Mutation: R286S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Strain: pROD / Gene: POL / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P04584, RNA-directed DNA polymerase | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: (NH4)2SO4, TRIS, DMSO, GLYCEROL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal grow | *PLUS Method: unknownDetails: Bird, L.E., (2003) Protein EExpression Purif., 27, 12. |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2001 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2.35→30 Å / Num. obs: 56142 / % possible obs: 100 % / Observed criterion σ(I): -1.5 / Redundancy: 11.3 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 16 | |||||||||
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.1 / Num. unique all: 5520 / % possible all: 100 | |||||||||
Reflection | *PLUS % possible obs: 100 % / Num. measured all: 631721 / Rmerge(I) obs: 0.128 | |||||||||
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 5520 / Rmerge(I) obs: 0.747 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hmv, 1rtj Resolution: 2.35→29.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2050186.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.9425 Å2 / ksol: 0.343704 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→29.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.43 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 53236 / Rfactor obs: 0.189 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.341 / Rfactor Rwork: 0.295 |