+Open data
-Basic information
Entry | Database: PDB / ID: 5xpw | |||||||||
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Title | Structure of amphioxus IgVJ-C2 molecule | |||||||||
Components | amphioxus IgVJ-C2 | |||||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin superfamily / dimmer | |||||||||
Function / homology | Function and homology information dendrite self-avoidance / cell-cell adhesion mediator activity / homophilic cell adhesion via plasma membrane adhesion molecules / axon guidance / axon / plasma membrane Similarity search - Function | |||||||||
Biological species | Branchiostoma floridae (Florida lancelet) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.003 Å | |||||||||
Authors | Chen, R. / Qi, J. / Zhang, N. / Zhang, L. / Yao, S. / Wu, Y. / Jiang, B. / Wang, Z. / Yuan, H. / Zhang, Q. / Xia, C. | |||||||||
Funding support | China, 2items
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Citation | Journal: J. Immunol. / Year: 2018 Title: Discovery and Analysis of Invertebrate IgVJ-C2 Structure from Amphioxus Provides Insight into the Evolution of the Ig Superfamily. Authors: Chen, R. / Zhang, L. / Qi, J. / Zhang, N. / Zhang, L. / Yao, S. / Wu, Y. / Jiang, B. / Wang, Z. / Yuan, H. / Zhang, Q. / Xia, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xpw.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xpw.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/5xpw ftp://data.pdbj.org/pub/pdb/validation_reports/xp/5xpw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19856.754 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-199 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Branchiostoma floridae (Florida lancelet) Gene: BRAFLDRAFT_122935 / Production host: Escherichia coli 042 (bacteria) / Strain (production host): 042 / References: UniProt: C3ZN36 |
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#2: 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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M lithium sulfate monohydrate, 0.1M BIS-TRIS (pH 5.5), 25% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98051 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98051 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 15493 / % possible obs: 98.2 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.439 / Num. measured obs: 15268 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.003→34.253 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 0.16 / Phase error: 23.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.747 Å2 / ksol: 0.411 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.003→34.253 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.5601 Å / Origin y: 4.4873 Å / Origin z: 10.6224 Å
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Refinement TLS group | Selection details: all |