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Yorodumi- PDB-1za6: The structure of an antitumor CH2-domain-deleted humanized antibody -
+Open data
-Basic information
Entry | Database: PDB / ID: 1za6 | ||||||
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Title | The structure of an antitumor CH2-domain-deleted humanized antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin fold / CH2-domain-deletion | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Larson, S.B. / Day, J.S. / Glaser, S. / Braslawsky, G. / McPherson, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The Structure of an Antitumor C(H)2-domain-deleted Humanized Antibody. Authors: Larson, S.B. / Day, J.S. / Glaser, S. / Braslawsky, G. / McPherson, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Combined use of AFM and X-ray diffraction to analyze crystals of an engineered, domain-deleted antibody Authors: Larson, S.B. / Kuznetsov, Y.G. / Day, J. / Zhou, J. / Glaser, S. / Braslawsky, G. / McPherson, A. | ||||||
History |
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Remark 999 | SEQUENCE There was no suitable sequence database match at time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1za6.cif.gz | 412 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1za6.ent.gz | 340.3 KB | Display | PDB format |
PDBx/mmJSON format | 1za6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/1za6 ftp://data.pdbj.org/pub/pdb/validation_reports/za/1za6 | 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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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Details | Chains A, B, C, D are the presumed biological unit / Chains E, F, G, H are the presumed biological unit |
-Components
#1: Antibody | Mass: 24206.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6GMV9 #2: Antibody | Mass: 36952.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6GMX6 |
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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: 3.29 Å3/Da / Density % sol: 62.3 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9194 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2003 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9194 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.13 Å / Num. obs: 76662 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.06 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.62 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 5 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BBJ; PDB ENTRY 1FC1 Resolution: 2.8→45.13 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 38542.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER / Details: USED NCS RESTRAINTS FOR EQUIVALENT CHAINS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.13 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→45.13 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |