+Open data
-Basic information
Entry | Database: PDB / ID: 7ff1 | ||||||
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Title | Structure of C34E136G/N36 | ||||||
Components |
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Keywords | VIRAL PROTEIN / HIV / envlope / 6HB | ||||||
Function / homology | Retroviral envelope protein / Retroviral envelope protein GP41-like / membrane => GO:0016020 / viral envelope / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane / Env polyprotein Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.689 Å | ||||||
Authors | Yu, D.W. / Qin, B. | ||||||
Citation | Journal: To Be Published Title: Structure of C34E136G/N36 Authors: Yu, D.W. / Qin, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ff1.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ff1.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 7ff1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ff1_validation.pdf.gz | 464.4 KB | Display | wwPDB validaton report |
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Full document | 7ff1_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 7ff1_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 7ff1_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/7ff1 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/7ff1 | HTTPS FTP |
-Related structure data
Related structure data | 1aikS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4152.843 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: C7F357 #2: Protein/peptide | Mass: 4205.553 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: BIS-Tris,Polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.689→43.74 Å / Num. obs: 28119 / % possible obs: 99.7 % / Redundancy: 6.628 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.95 |
Reflection shell | Resolution: 1.689→1.79 Å / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 4478 / CC1/2: 0.757 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AIK Resolution: 1.689→43.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.85 Å2 / Biso mean: 44.4355 Å2 / Biso min: 24.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.689→43.74 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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