[English] 日本語
Yorodumi- PDB-1qlr: CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A HUMAN MONOCLONAL IgM C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qlr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A HUMAN MONOCLONAL IgM COLD AGGLUTININ | |||||||||
Components |
| |||||||||
Keywords | IMMUNOGLOBULIN / AUTOANTIBODY / COLD AGGLUTININ / HUMAN IGM FAB FRAGMENT | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | |||||||||
Authors | Carvalho, J.G. / Cauerhff, A. / Goldbaum, F. / Leoni, J. / Polikarpov, I. | |||||||||
Citation | Journal: J Immunol. / Year: 2000 Title: Three-dimensional structure of the Fab from a human IgM cold agglutinin. Authors: Cauerhff, A. / Braden, B.C. / Carvalho, J.G. / Aparicio, R. / Polikarpov, I. / Leoni, J. / Goldbaum, F.A. #1: Journal: Protein Pept.Lett. / Year: 1998 Title: Crystallization and Preliminary Diffraction Studies of a Human Fabm with Anti-I Activity Authors: Cauerhff, A. / Polikarpov, I. / Mathov, I. / Abatangelo, C. / Plotkin, L. / Goldbaum, F.A. / Leoni, J. #2: Journal: J.Biol.Chem. / Year: 1991 Title: The Primary Structure of the Fab Fragment of Protein Kau, a Monoclonal Immunoglobulin M Cold Agglutinin Authors: Leoni, J. / Ghiso, J. / Goni, F. / Frangione, B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qlr.cif.gz | 176.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qlr.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1qlr ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1qlr | HTTPS FTP |
---|
-Related structure data
Related structure data | 1dn0C 1dfbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Antibody | Mass: 23301.770 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source Details: FAB FRAGMENT WAS PREPARED BY DIGESTION OF MONOCLONAL IGM KAU PURIFIED FROM PATIENT WITH AIHA. Source: (natural) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / Cellular location: EXTRACELLULARGlossary of biology / References: PIR: A23746, UniProt: Q6PJF2*PLUS #2: Antibody | Mass: 25191.094 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source Details: FAB FRAGMENT WAS PREPARED BY DIGESTION OF MONOCLONAL IGM KAU PURIFIED FROM PATIENT WITH AIHA. Source: (natural) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / Cellular location: EXTRACELLULARGlossary of biology / References: PIR: B23746 #3: Polysaccharide | Source method: isolated from a genetically manipulated source Sequence details | THE SEQUENCE IS DESCRIBED IN J.LEONI,J.GHISO,F.GONI,B.FRANGIONE, J.BIOL.CHEM. 1991 V.266 2836-42 ...THE SEQUENCE IS DESCRIBED IN J.LEONI,J.GHISO,F.GONI,B.FRANGIONE, J.BIOL.CHEM. 1991 V.266 2836-42 THE CYS TO GLY CONFLICTS DETAILED IN SEQADV ARE DIFFERENCE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: 14%(W/W) PEG 8000, 0.1 M SODIUM HEPES PH 7.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop / Details: Cauerhff, A., (1998) Protein Pept.Lett., 5, 177. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 291 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→13.1 Å / Num. obs: 31329 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 |
Reflection shell | Resolution: 2.83→2.89 Å / % possible all: 95.4 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DFB Resolution: 2.83→13.1 Å / SU B: 12.46 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.84 / ESU R Free: 0.36 Details: RESIDUES B,D 135 - 143, B,D 195 - 201, B,D 226 - 232, WERE NOT MODELED DUE TO LACK OF ELETRONIC DENSIT MAP. THE CONFORMATION OF RESIDUES B,D 202 - 204 SHOULD BE CONSIDERED AS A TENTATIVE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→13.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |