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Yorodumi- PDB-1dql: CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dql | |||||||||
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Title | CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI-PEPTIDE ANTIBODY | |||||||||
Components | (IGM MEZ IMMUNOGLOBULIN) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / ANTIBODY / IgM / Fv | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | |||||||||
Authors | Ramsland, P.A. / Shan, L. / Moomaw, C.R. / Slaughter, C.A. / Guddat, L.W. / Edmundson, A.B. | |||||||||
Citation | Journal: Mol.Immunol. / Year: 2000 Title: An unusual human IgM antibody with a protruding HCDR3 and high avidity for its peptide ligands. Authors: Ramsland, P.A. / Shan, L. / Moomaw, C.R. / Slaughter, C.A. / Fan, Z. / Guddat, L.W. / Edmundson, A.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dql.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dql.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dql ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dql | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The Mez Fv is a non-covalent heterodimer of VL (chain L) and VH (chain H) |
-Components
#1: Antibody | Mass: 11527.743 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN VARIABLE DOMAIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 13214.604 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN VARIABLE DOMAIN FRAGMENT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#3: 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: 2.72 Å3/Da / Density % sol: 55.2 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: microseeding, sitting drop / pH: 7 Details: 6-8% (W/V) PEG 8000, 0.05% (W/V) SODIUM AZIDE, pH 7.0, MICROSEEDING, SITTING DROP, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 19, 1990 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→20 Å / Num. all: 7111 / Num. obs: 7111 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.25 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.58→2.75 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.167 / % possible all: 40 |
Reflection | *PLUS Highest resolution: 2.6 Å / % possible obs: 83.4 % |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.76 Å / % possible obs: 40.6 % |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.31 Å2 / ksol: 0.252 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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