- PDB-5xau: Crystal structure of integrin binding fragment of laminin-511 -
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Basic information
Entry
Database: PDB / ID: 5xau
Title
Crystal structure of integrin binding fragment of laminin-511
Components
(Laminin subunit ...) x 3
Keywords
CELL ADHESION / laminin / integrin / extracellular matrix protein
Function / homology
Function and homology information
laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions ...laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / L1CAM interactions / trunk neural crest cell migration / basement membrane assembly / hemidesmosome assembly / postsynapse organization / positive regulation of integrin-mediated signaling pathway / morphogenesis of embryonic epithelium / morphogenesis of a polarized epithelium / tissue development / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / endoderm development / branching involved in salivary gland morphogenesis / protein complex involved in cell-matrix adhesion / regulation of epithelial cell proliferation / odontogenesis / muscle organ development / MET activates PTK2 signaling / extracellular matrix structural constituent / branching involved in ureteric bud morphogenesis / maintenance of blood-brain barrier / positive regulation of muscle cell differentiation / endodermal cell differentiation / odontogenesis of dentin-containing tooth / regulation of embryonic development / positive regulation of cell adhesion / Non-integrin membrane-ECM interactions / basement membrane / hair follicle development / ECM proteoglycans / cilium assembly / extracellular matrix disassembly / regulation of cell adhesion / synaptic cleft / regulation of cell migration / Degradation of the extracellular matrix / substrate adhesion-dependent cell spreading / positive regulation of epithelial cell proliferation / protein localization to plasma membrane / integrin-mediated signaling pathway / animal organ morphogenesis / Post-translational protein phosphorylation / axon guidance / lung development / neuromuscular junction / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cell migration / integrin binding / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / cell adhesion / positive regulation of cell migration / endoplasmic reticulum lumen / glutamatergic synapse / structural molecule activity / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function
Laminin IV type B domain / Laminin IV type B / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. ...Laminin IV type B domain / Laminin IV type B / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / Laminin G domain profile. / TNFR/NGFR cysteine-rich region / Laminin G domain / Laminin G domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9 Å / Relative weight: 1
Reflection
Resolution: 1.8→50 Å / Num. obs: 164205 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.065 / Net I/σ(I): 29.08
Reflection shell
Resolution: 1.8→1.83 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.47 / Rsym value: 1.14 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0158
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→49.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.081 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23726
8245
5 %
RANDOM
Rwork
0.20165
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obs
0.20343
155954
99.78 %
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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