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Yorodumi- PDB-5bzm: Crystal structure of the murine cd44 hyaluronan binding domain co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bzm | ||||||
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Title | Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule | ||||||
Components | CD44 antigen | ||||||
Keywords | PROTEIN BINDING / Link module | ||||||
Function / homology | Function and homology information Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process ...Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / wound healing involved in inflammatory response / positive regulation of adaptive immune response / positive regulation of neutrophil apoptotic process / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / cargo receptor activity / wound healing, spreading of cells / epidermal growth factor receptor binding / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / channel regulator activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / microvillus / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / Wnt signaling pathway / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / neuron projection development / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / apical plasma membrane / membrane raft / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / cell surface / protein-containing complex / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | ||||||
Authors | Liu, L.K. / Finzel, B.C. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule Authors: Liu, L.K. / Finzel, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bzm.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bzm.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 5bzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bzm_validation.pdf.gz | 753.9 KB | Display | wwPDB validaton report |
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Full document | 5bzm_full_validation.pdf.gz | 754.9 KB | Display | |
Data in XML | 5bzm_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5bzm_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/5bzm ftp://data.pdbj.org/pub/pdb/validation_reports/bz/5bzm | HTTPS FTP |
-Related structure data
Related structure data | 5bzcC 5bzeC 5bzfC 5bzgC 5bzhC 5bziC 5bzjC 5bzkC 5bzlC 5bznC 5bzoC 5bzpC 5bzqC 5bzrC 5bzsC 5bztC 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: Protein | Mass: 16855.803 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 21-171 / Mutation: H23M; Q24N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Ly-24 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): 4 / References: UniProt: P15379 |
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#2: Chemical | ChemComp-4X8 / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-SO4 / |
#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: 2.13 Å3/Da / Density % sol: 42.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG MME 5000, MES, (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2013 | ||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.25→40.758 Å / Num. obs: 36505 / % possible obs: 94.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11 / Num. measured all: 119038 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→40.758 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2281 / WRfactor Rwork: 0.2086 / FOM work R set: 0.8667 / SU B: 0.825 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0553 / SU Rfree: 0.0567 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.61 Å2 / Biso mean: 13.516 Å2 / Biso min: 4.63 Å2
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Refinement step | Cycle: final / Resolution: 1.25→40.758 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.249→1.282 Å / Total num. of bins used: 20
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