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Yorodumi- PDB-4nzu: Crystal structure of the primary monoclonal antibody 13PL Fab' fr... -
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-Basic information
Entry | Database: PDB / ID: 4nzu | ||||||
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Title | Crystal structure of the primary monoclonal antibody 13PL Fab' from a multiple myeloma patient | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody Fab / multiple myeloma / primary antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Zhu, X. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 2014 Title: A structurally distinct human mycoplasma protein that generically blocks antigen-antibody union. Authors: Rajesh K Grover / Xueyong Zhu / Travis Nieusma / Teresa Jones / Isabel Boreo / Amanda S MacLeod / Adam Mark / Sherry Niessen / Helen J Kim / Leopold Kong / Nacyra Assad-Garcia / Keehwan Kwon ...Authors: Rajesh K Grover / Xueyong Zhu / Travis Nieusma / Teresa Jones / Isabel Boreo / Amanda S MacLeod / Adam Mark / Sherry Niessen / Helen J Kim / Leopold Kong / Nacyra Assad-Garcia / Keehwan Kwon / Marta Chesi / Vaughn V Smider / Daniel R Salomon / Diane F Jelinek / Robert A Kyle / Richard B Pyles / John I Glass / Andrew B Ward / Ian A Wilson / Richard A Lerner / Abstract: We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known ...We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known protein structures, as does its mechanism of antibody binding. Protein M binds with high affinity to all types of human and nonhuman immunoglobulin G, predominantly through attachment to the conserved portions of the variable region of the κ and λ light chains. Protein M blocks antibody-antigen union, likely because of its large C-terminal domain extending over the antibody-combining site, blocking entry to large antigens. Similar to the other immunoglobulin-binding proteins such as Protein A, Protein M as well as its orthologs in other Mycoplasma species could become invaluable reagents in the antibody field. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nzu.cif.gz | 301.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nzu.ent.gz | 246.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nzu_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 4nzu_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 4nzu_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4nzu_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/4nzu ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nzu | HTTPS FTP |
-Related structure data
Related structure data | 5834C 5835C 5836C 4nzrC 4nztC 1hilS C: citing same article (ref.) 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: 23174.680 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood | ||||
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#2: Antibody | Mass: 23482.074 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / | #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: 2.26 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1 M citric acid, pH 4.0, 1.0 M lithium chloride, 23% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→63.287 Å / Num. obs: 126314 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rsym value: 0.05 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.62 / % possible all: 73.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HIL Resolution: 1.2→63.287 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.038 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→63.287 Å
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Refine LS restraints |
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