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Yorodumi- PDB-1fl6: THE HAPTEN COMPLEXED GERMLINE PRECURSOR TO SULFIDE OXIDASE CATALY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fl6 | ||||||
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Title | THE HAPTEN COMPLEXED GERMLINE PRECURSOR TO SULFIDE OXIDASE CATALYTIC ANTIBODY 28B4 | ||||||
Components | (ANTIBODY GERMLINE PRECURSOR TO 28B4) x 2 | ||||||
Keywords | IMMUNE SYSTEM / catalytic antibody / germline antibody / sulfide oxidase | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-AAH Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Yin, J. / Mundorff, E.C. / Yang, P.L. / Wendt, K.U. / Hanway, D. / Stevens, R.C. / Schultz, P.G. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: A comparative analysis of the immunological evolution of antibody 28B4. Authors: Yin, J. / Mundorff, E.C. / Yang, P.L. / Wendt, K.U. / Hanway, D. / Stevens, R.C. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fl6.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fl6.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 1fl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fl6_validation.pdf.gz | 945.7 KB | Display | wwPDB validaton report |
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Full document | 1fl6_full_validation.pdf.gz | 984.3 KB | Display | |
Data in XML | 1fl6_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 1fl6_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/1fl6 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/1fl6 | HTTPS FTP |
-Related 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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Details | The bioliogical assembly is constructed from chain L and H. Chains A and B contruct another biological unit related through non-crystallographic symmetry |
-Components
#1: Antibody | Mass: 23789.566 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN (CHAINS L AND A) / Mutation: S25F, P40S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 23386.072 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN (CHAINS H AND B) / Mutation: V12G, M34F, S35N, V37A, N53K, S76G, D95W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | |
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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: 2.34 Å3/Da / Density % sol: 47.35 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 100 mM Tris 800 mM NaCl 26% PEG 4000 4 mM hapten, pH 7.5, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 23576 / Num. obs: 20056 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.39 / Num. unique all: 1960 / % possible all: 91.9 |
Reflection | *PLUS Num. measured all: 47152 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 91.9 % |
-Processing
Software |
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Refinement | Resolution: 2.8→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 129832.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 12.94 Å2 / ksol: 0.295 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 9.8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.373 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.324 |