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Yorodumi- PDB-4ah9: Parallel screening of a low molecular weight compound library: do... -
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-Basic information
Entry | Database: PDB / ID: 4ah9 | ||||||
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Title | Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification | ||||||
Components | INTEGRASE | ||||||
Keywords | TRANSFERASE / FRAGMENT SCREENING | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wielens, J. / Heady, S.J. / Rhodes, D.I. / Mulder, R.J. / Dolezal, O. / Deadman, J.J. / Newman, J. / Chalmers, D.K. / Parker, M.W. / Peat, T.S. / Scanlon, M.J. | ||||||
Citation | Journal: J.Biomol.Screen / Year: 2013 Title: Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification? Authors: Wielens, J. / Headey, S.J. / Rhodes, D.I. / Mulder, R.J. / Dolezal, O. / Deadman, J.J. / Newman, J. / Chalmers, D.K. / Parker, M.W. / Peat, T.S. / Scanlon, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ah9.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ah9.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ah9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ah9_validation.pdf.gz | 1017.3 KB | Display | wwPDB validaton report |
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Full document | 4ah9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4ah9_validation.xml.gz | 20 KB | Display | |
Data in CIF | 4ah9_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/4ah9 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/4ah9 | HTTPS FTP |
-Related structure data
Related structure data | 3vq4C 3vq5C 3vq6C 3vq7C 3vq8C 3vq9C 3vqaC 3vqbC 3vqcC 3vqdC 3vqeC 3vqpC 3vqqC 4ahrC 4ahsC 4ahtC 4ahuC 4ahvC 1bi4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20044.672 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 1197-1359 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS / Strain: TYPE 1 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P12497, nicotinamide-nucleotide adenylyltransferase |
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-Non-polymers , 7 types, 216 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 1203 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 1286 TO ASP ...ENGINEERED |
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Nonpolymer details | LIGAND (0MB): FRAGMENT FROM MAYBRIDGE LIBRARY |
Sequence details | N-TERMINAL HIS-TAG AND C56S, F139D, F185H |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 100 MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 M TO 1.5 M AMMONIUM SULFATE. THE PROTEIN WAS IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS ...Details: 100 MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 M TO 1.5 M AMMONIUM SULFATE. THE PROTEIN WAS IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95362 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95362 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45 Å / Num. obs: 40414 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.7 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BI4 Resolution: 1.7→61.08 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.861 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.925 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→61.08 Å
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Refine LS restraints |
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