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Yorodumi- PDB-2f58: IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f58 | ||||||
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Title | IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120) (MN ISOLATE) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / HIV-1 / GP120 / V3 | ||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / immune response / extracellular space Similarity search - Function | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f58.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f58.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 2f58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f58 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f58 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23573.012 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01666*PLUS |
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#2: Antibody | Mass: 24864.744 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C |
#3: Protein/peptide | Mass: 1027.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS MOLECULE WAS CHEMICALLY SYNTHESIZED |
#4: Chemical | ChemComp-ARN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 5 / Details: 16% PEG4000, 0.2M IMIDAZOLE MALATE, PH 5.0 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 15, 1992 |
Radiation | Monochromator: GRAPHITE / 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→24 Å / Num. obs: 12923 / % possible obs: 91.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.076 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.8→3.02 Å / Redundancy: 1.99 % / Mean I/σ(I) obs: 1 / Rsym value: 0.288 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FAB 58.2 PORTION OF FAB 58.2/SER-LOOP PEPTIDE COMPLEX Resolution: 2.8→24 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 26.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→3.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 5
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Xplor file |
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