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Yorodumi- PDB-6w4y: Structure of full-length human lambda-6A light chain JTO in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w4y | ||||||
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Title | Structure of full-length human lambda-6A light chain JTO in complex with hydantoin stabilizer | ||||||
Components | JTO light chain | ||||||
Keywords | IMMUNE SYSTEM / amyloidosis | ||||||
Function / homology | Chem-7ZW / PHOSPHATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Yan, N.L. / Morgan, G.J. / Kelly, J.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2020 Title: Structural basis for the stabilization of amyloidogenic immunoglobulin light chains by hydantoins. Authors: Yan, N.L. / Santos-Martins, D. / Rennella, E. / Sanchez, B.B. / Chen, J.S. / Kay, L.E. / Wilson, I.A. / Morgan, G.J. / Forli, S. / Kelly, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w4y.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w4y.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 6w4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/6w4y ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w4y | HTTPS FTP |
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-Related structure data
Related structure data | 6mg4S 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: 23211.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-7ZW / | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.71 Å3/Da / Density % sol: 54.61 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 and 0.25 M NH4H2PO4 at 23 degrees C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976484 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→44.65 Å / Num. obs: 39919 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 1 / Rpim(I) all: 0.025 / Rsym value: 0.066 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.91→2.01 Å / Redundancy: 8.1 % / Num. unique obs: 5702 / CC1/2: 0.92 / Rpim(I) all: 0.025 / Rsym value: 0.066 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MG4 Resolution: 1.91→44.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.023 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.142 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 146.56 Å2 / Biso mean: 33.161 Å2 / Biso min: 17.19 Å2
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Refinement step | Cycle: final / Resolution: 1.91→44.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.959 Å / Rfactor Rfree error: 0
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