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Yorodumi- PDB-5zmj: Crystal structure of the Fab region of a neutralizing fully human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zmj | ||||||
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Title | Crystal structure of the Fab region of a neutralizing fully human antibody against GM-CSF | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / fully human antibody / GM-CSF | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Angkawidjaja, C. / Torashima, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Crystal structure of the Fab region of a neutralizing antibody against granulocyte-macrophage colony-stimulating factor. Authors: Angkawidjaja, C. / Torashima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zmj.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zmj.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zmj_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 5zmj_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 5zmj_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 5zmj_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/5zmj ftp://data.pdbj.org/pub/pdb/validation_reports/zm/5zmj | HTTPS FTP |
-Related structure data
Related structure data | 4eowS 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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-Components
#1: Antibody | Mass: 26751.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: P01857 (UniProt) is referred. / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) | ||||
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#2: Antibody | Mass: 24952.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: P0DOY2(UniProt) is referred. / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / #5: 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: 2.46 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→46.37 Å / Num. obs: 43756 / % possible obs: 98.1 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.81→1.85 Å / Rmerge(I) obs: 0.171 / Num. unique obs: 3133 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EOW Resolution: 1.81→46.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.006 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.529 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→46.37 Å
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Refine LS restraints |
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