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Yorodumi- PDB-1fl5: THE UNLIGANDED GERMLINE PRECURSOR TO THE SULFIDE OXIDASE CATALYTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fl5 | ||||||
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Title | THE UNLIGANDED GERMLINE PRECURSOR TO THE SULFIDE OXIDASE CATALYTIC ANTIBODY 28B4. | ||||||
Components | (ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4) x 2 | ||||||
Keywords | IMMUNE SYSTEM / catalytic antibody / germline antibody / sulfide oxidase | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 | 1fl5.cif.gz | 176 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fl5.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fl5_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 1fl5_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 1fl5_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 1fl5_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/1fl5 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/1fl5 | 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, N53L, S76G, D95W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | #4: 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: 2.14 Å3/Da / Density % sol: 42.58 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 3.9 Details: 100 mM ammonium sulfate 50 mM sodium acetate 10% PEG 2000 MME, pH 3.9, VAPOR DIFFUSION, temperature 277.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 100 K / 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: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 51231 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.221 / Num. unique all: 4849 / % possible all: 70.5 |
Reflection | *PLUS Num. measured all: 109371 |
Reflection shell | *PLUS Highest resolution: 2.07 Å / Lowest resolution: 2.15 Å / % possible obs: 95.2 % |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 376700.18 / 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: 31.89 Å2 / ksol: 0.298 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / 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: 10.1 % / Rfactor obs: 0.226 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.318 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.256 |