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Yorodumi- PDB-1clz: IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1clz | |||||||||
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Title | IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER | |||||||||
Components | (IGG FAB (IGG3, KAPPA)) x 2 | |||||||||
Keywords | IMMUNOGLOBULIN / IMMUNOGLOBULIN C REGION / GLYCOPROTEIN / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information immunoglobulin receptor binding / membrane => GO:0016020 / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | |||||||||
Authors | Sheriff, S. / Bajorath, J. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: The x-ray structure of an anti-tumour antibody in complex with antigen. Authors: Jeffrey, P.D. / Bajorath, J. / Chang, C.Y. / Yelton, D. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Analysis of the Monoclonal Anti-Tumor Antibody Br96 and its Complex with the Lewis Y Determinant Authors: Chang, C.Y. / Jeffrey, P.D. / Bajorath, J. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1clz.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1clz.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 1clz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1clz ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1clz | HTTPS FTP |
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-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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-Components
#1: Antibody | Mass: 24246.910 Da / Num. of mol.: 1 / Fragment: FRAGMENT (MBR96) / Source method: isolated from a natural source / Details: HYBRIDIZED WITH P2X63-AG MOUSE / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: PIR: PC4203 |
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#2: Antibody | Mass: 23759.754 Da / Num. of mol.: 1 / Fragment: FRAGMENT (MBR96) / Source method: isolated from a natural source / Details: HYBRIDIZED WITH P2X63-AG MOUSE / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P22436 |
#3: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis Y antigen / beta anomer |
#4: Chemical | ChemComp-NON / |
Sequence details | THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN ...THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN (RESIDUES 1 - 231) HAS BEEN ASSIGNED CHAIN INDICATOR H. THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: pH 7.8 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: Chang, C.Y., (1994) J.Mol.Biol., 235, 372. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jan 1, 1993 / Details: MIRROR (SUPPER 6 CM) |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→38.1 Å / Num. obs: 9937 / % possible obs: 73.9 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.78→2.95 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.151 / % possible all: 43.8 |
Reflection | *PLUS Num. measured all: 23962 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 43.8 % |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / Cross valid method: EX POST FACTO / σ(F): 1
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Displacement parameters | Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.87 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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