+Open data
-Basic information
Entry | Database: PDB / ID: 1qbz | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE SIV GP41 ECTODOMAIN AT 1.47 A | ||||||
Components | PROTEIN (SIV GP41 ECTODOMAIN) | ||||||
Keywords | ENVELOPE GLYCOPROTEIN / SIV / HIV / GP41 / MEMBRANE FUSION / PEPTIDE INHIBITOR / SIV ENVELOPE GLYCOPROTEIN GP41 | ||||||
Function / homology | Function and homology information membrane fusion involved in viral entry into host cell / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Simian immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR, molecular replacement / Resolution: 1.47 Å | ||||||
Authors | Yang, Z.-N. / Mueser, T.C. / Kaufman, J. / Stahl, S.J. / Wingfield, P.T. / Hyde, C.C. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 1999 Title: The crystal structure of the SIV gp41 ectodomain at 1.47 A resolution. Authors: Yang, Z.N. / Mueser, T.C. / Kaufman, J. / Stahl, S.J. / Wingfield, P.T. / Hyde, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qbz.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qbz.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qbz ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qbz | HTTPS FTP |
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-Related structure data
Related structure data | 1mofS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14431.267 Da / Num. of mol.: 3 / Fragment: SIV GP41 ECTODOMAIN 27-149 / Mutation: C86A, C92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Strain: MAC239 / Cellular location: VIRAL MEMBRANE / Production host: Escherichia coli (E. coli) / References: GenBank: 431600, UniProt: E7CWP5*PLUS #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 1.78 Å3/Da / Density % sol: 30.8 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.25 Details: 14-25% MPD (2-METHYL-2,4- PENTANEDIOL) 140-220 MM NACL, 20-40 MM SODIUM ACETATE, pH 4.25 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 3 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97564 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97564 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→15 Å / Num. obs: 49553 / % possible obs: 89.9 % / Observed criterion σ(I): 0.5 / Redundancy: 8.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.6 / % possible all: 70.9 |
Reflection | *PLUS Num. measured all: 412245 |
Reflection shell | *PLUS % possible obs: 78.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR, molecular replacement Starting model: POLY ALANINE MODEL (RESIDUES 46-74) OF MMLV TRANSMEMBRANE TRIMERIC CORE (1MOF) Resolution: 1.47→15 Å / Num. parameters: 28962 / Num. restraintsaints: 36906 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER Details: NO NCS RESTRAINS WERE APPLIED DURING REFINEMENT CAUTION SHOULD BE TAKEN IN INTERPRETING THOSE RESIDUES WITH EQUIVALENT ISOTROPIC B FACTORS HIGHER THAN 60S.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. V. 91 (1973) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 37 / Occupancy sum hydrogen: 2609 / Occupancy sum non hydrogen: 3046 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(I): 2 / % reflection Rfree: 5 % / Rfactor all: 0.16 / Rfactor Rwork: 0.152 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.267 |