[English] 日本語
Yorodumi- PDB-3f58: IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f58 | ||||||
---|---|---|---|---|---|---|---|
Title | IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120 (MN ISOLATE); H315S MUTATION | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / HIV-1 / GP120 / V3 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Stanfield, R.L. / Cabezas, E. / Satterthwait, A.C. / Stura, E.A. / Profy, A.T. / Wilson, I.A. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. Authors: Stanfield, R. / Cabezas, E. / Satterthwait, A. / Stura, E. / Profy, A. / Wilson, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f58.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f58.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 3f58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f58 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f58 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1f58C 2f58C 1acyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23501.934 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN OF FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C |
---|---|
#2: Antibody | Mass: 24864.744 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN OF FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C |
#3: Protein/peptide | Mass: 976.070 Da / Num. of mol.: 1 / Fragment: RESIDUES 315-324 FROM HIV-1 GP120 / Mutation: H315S / Source method: obtained synthetically Details: 12 RESIDUE HYDRAZONE-LINKED CYCLIC PEPTIDE WAS CHEMICALLY SYNTHESIZED FROM RESIDUES 316-324 OF HIV-1 GP120 STRAIN MN. |
#4: Water | ChemComp-HOH / |
Sequence details | THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H. ...THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1992 / Details: SUPPER DOUBLE MIRRORS |
Radiation | Monochromator: SUPPER DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.8 Å / Num. obs: 13951 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.1 Å2 / Rsym value: 0.072 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.218 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 47266 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 97.7 % / Num. unique obs: 2259 / Num. measured obs: 9337 / Rmerge(I) obs: 0.218 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FAB PORTION OF 1ACY Resolution: 2.8→48 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.377 |