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Yorodumi- PDB-7lmq: Structure of full-length human lambda-6A light chain JTO in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lmq | |||||||||
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Title | Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 62 [4-methyl-3-(morpholinomethyl)-7-(1-phenylethoxy)-2H-chromen-2-one] | |||||||||
Components | JTO light chain | |||||||||
Keywords | IMMUNE SYSTEM / amyloidosis | |||||||||
Function / homology | Chem-9ZW / 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. / Wilson, I.A. / Kelly, J.W. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of Potent Coumarin-Based Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains Using Structure-Based Design. Authors: Yan, N.L. / Santos-Martins, D. / Nair, R. / Chu, A. / Wilson, I.A. / Johnson, K.A. / Forli, S. / Morgan, G.J. / Petrassi, H.M. / 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 | 7lmq.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lmq.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 7lmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lmq_validation.pdf.gz | 790.1 KB | Display | wwPDB validaton report |
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Full document | 7lmq_full_validation.pdf.gz | 791.8 KB | Display | |
Data in XML | 7lmq_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 7lmq_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/7lmq ftp://data.pdbj.org/pub/pdb/validation_reports/lm/7lmq | HTTPS FTP |
-Related structure data
Related structure data | 7lmnC 7lmoC 7lmpC 7lmrC 6mg5S S: Starting model for refinement C: citing same article (ref.) |
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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-9ZW / | #3: Chemical | #4: 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: 2.7 Å3/Da / Density % sol: 54.39 % |
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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 27, 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→44.63 Å / Num. obs: 39458 / % possible obs: 99.1 % / Redundancy: 7.7 % / Biso Wilson estimate: 17 Å2 / CC1/2: 1 / Rpim(I) all: 0.037 / Rsym value: 0.096 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.91→2.01 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5381 / CC1/2: 0.95 / Rpim(I) all: 0.278 / Rsym value: 1.033 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MG5 Resolution: 1.91→44.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 211.56 Å2 / Biso mean: 24.175 Å2 / Biso min: 11.1 Å2
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Refinement step | Cycle: final / Resolution: 1.91→44.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.958 Å / Rfactor Rfree error: 0
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