+Open data
-Basic information
Entry | Database: PDB / ID: 1igt | |||||||||
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Title | STRUCTURE OF IMMUNOGLOBULIN | |||||||||
Components | (IGG2A INTACT ANTIBODY - MAB231) x 2 | |||||||||
Keywords | IMMUNOGLOBULIN / INTACT IMMUNOGLOBULIN V REGION C REGION | |||||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Harris, L.J. / Larson, S.B. / Hasel, K.W. / McPherson, A. | |||||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Refined structure of an intact IgG2a monoclonal antibody. Authors: Harris, L.J. / Larson, S.B. / Hasel, K.W. / McPherson, A. #1: Journal: Nature / Year: 1992 Title: The Three-Dimensional Structure of an Intact Monoclonal Antibody for Canine Lymphoma Authors: Harris, L.J. / Larson, S.B. / Hasel, K.W. / Day, J. / Greenwood, A. / McPherson, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1igt.cif.gz | 318 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1igt.ent.gz | 262.4 KB | Display | PDB format |
PDBx/mmJSON format | 1igt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1igt_validation.pdf.gz | 600.8 KB | Display | wwPDB validaton report |
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Full document | 1igt_full_validation.pdf.gz | 647 KB | Display | |
Data in XML | 1igt_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 1igt_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/1igt ftp://data.pdbj.org/pub/pdb/validation_reports/ig/1igt | HTTPS FTP |
-Related structure data
Related structure data | 1fc1S 1mcpS 2hfl S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THERE IS ONE ENTIRE ANTIBODY MOLECULE PER ASYMMETRIC UNIT. |
-Components
#1: Antibody | Mass: 23420.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C #2: Antibody | Mass: 49294.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HYBRIDOMA MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01863 #3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source Sequence details | THE INTACT ANTIBODY IS NUMBERED ACCORDING TO THE CONVENTION OF E. KABAT [KABAT ET AL. (1991) ...THE INTACT ANTIBODY IS NUMBERED ACCORDING TO THE CONVENTION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 13 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63 % Description: THE MULTIWIRE AND SYNCHROTRON DATA SETS WERE CUT AT F > 4SIGMA, AND THEN MERGED TO YIELD THE FINAL REDUCED DATA SET OF 41371 UNIQUE REFLECTIONS AT 2.8-20 A; RMERGE = 6.7%. THIS COMBINED ...Description: THE MULTIWIRE AND SYNCHROTRON DATA SETS WERE CUT AT F > 4SIGMA, AND THEN MERGED TO YIELD THE FINAL REDUCED DATA SET OF 41371 UNIQUE REFLECTIONS AT 2.8-20 A; RMERGE = 6.7%. THIS COMBINED DATA WAS USED FOR REFINEMENT. | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / pH: 8 Details: 7 MICROLITERS OF 4.3 MG/ML MAB231, 3 MICROLITERS 50 MILLIMOLAR TRIS PH 8.0, AND 7 MICROLITERS 4% PEG 3350 EQUILIBRATED AGAINST 25 ML RESERVOIRS OF 4% PEG 3350, AT 18 DEGREE CELSIUS (SANDWICH ...Details: 7 MICROLITERS OF 4.3 MG/ML MAB231, 3 MICROLITERS 50 MILLIMOLAR TRIS PH 8.0, AND 7 MICROLITERS 4% PEG 3350 EQUILIBRATED AGAINST 25 ML RESERVOIRS OF 4% PEG 3350, AT 18 DEGREE CELSIUS (SANDWICH PLATE)., temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion / Details: Larson, S., (1991) J. Mol. Biol., 222, 17. / PH range low: 8.2 / PH range high: 7.8 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 1, 1992 |
Radiation | Monochromator: SUPPER GRAPHITE CRYSTAL ASYMMETRIC CUT TRIANGULAR BENT CRYSTAL (SI-111) Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→76.1 Å / Num. obs: 47595 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 45.5 Å2 / Rsym value: 0.1 / Net I/σ(I): 7.1 |
Reflection | *PLUS Num. measured all: 200000 / Rmerge(I) obs: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: VL:VH DOMAIN PAIR OF PDB ENTRY 1MCP, CL:CH1 DOMAIN PAIR OF ENTRY 2HFL, FC FRAGMENT OF ENTRY 1FC1 Resolution: 2.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 Details: BULK SOLVENT MODEL USED GROUP 1 POSITIONAL (CL) (A) : 0.05 ; 200 GROUP 2 POSITIONAL (CH1) (A) : 0.05 ; 200 GROUP 3 POSITIONAL (CH2) (A) : 0.06 ; 200 GROUP 4 POSITIONAL (CH3) (A) : 0.05 ; 200 ...Details: BULK SOLVENT MODEL USED GROUP 1 POSITIONAL (CL) (A) : 0.05 ; 200 GROUP 2 POSITIONAL (CH1) (A) : 0.05 ; 200 GROUP 3 POSITIONAL (CH2) (A) : 0.06 ; 200 GROUP 4 POSITIONAL (CH3) (A) : 0.05 ; 200 BACKBONE ATOMS ONLY WERE RESTRAINED BY NCS AND RESIDUES INVOLVED IN PACKING WERE NOT RESTRAINED. NCS B-FACTOR RESTRAINTS WERE NOT EMPLOYED.
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Displacement parameters | Biso mean: 52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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