[English] 日本語
Yorodumi- PDB-3nxe: X-ray structure of ester chemical analogue 'covalent dimer' [Ile5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nxe | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with MVT-101 inhibitor | ||||||
Components | protease covalent dimer | ||||||
Keywords | hydrolase/hydrolase inhibitor / beta-barrel / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Torbeev, V.Y. / Kent, S.B.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Authors: Torbeev, V.Y. / Raghuraman, H. / Hamelberg, D. / Tonelli, M. / Westler, W.M. / Perozo, E. / Kent, S.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3nxe.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3nxe.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 3nxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nxe_validation.pdf.gz | 709 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3nxe_full_validation.pdf.gz | 711.8 KB | Display | |
Data in XML | 3nxe_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3nxe_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/3nxe ftp://data.pdbj.org/pub/pdb/validation_reports/nx/3nxe | HTTPS FTP |
-Related structure data
Related structure data | 3fsmC 3hauC 3hawC 3hboC 3hdkC 3hloC 3iawC 3ka2C 3nwqC 3nwxC 3nxnC 3nygC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21892.635 Da / Num. of mol.: 1 / Fragment: covalent dimer HIV-1 protease / Mutation: Ile50'[O-Ile] / Source method: obtained synthetically / Details: chemical protein synthesis / References: UniProt: O38716*PLUS, HIV-1 retropepsin | ||
---|---|---|---|
#2: Chemical | ChemComp-2NC / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Citrate, 0.2 M Sodium Phosphate, 30% (w/v) Ammonium Sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2007 |
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 24541 / Num. obs: 24296 / % possible obs: 99 % / Observed criterion σ(F): 103.2 / Observed criterion σ(I): 103.2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.04 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.22 / % possible all: 98 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.801 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.366 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.607→1.649 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|