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- PDB-5nay: Crystal structures of homooligomers of collagen type IV. alpha1NC1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nay | |||||||||
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Title | Crystal structures of homooligomers of collagen type IV. alpha1NC1 | |||||||||
![]() | Collagen alpha-1(IV) chain | |||||||||
![]() | STRUCTURAL PROTEIN / Non-collagenous domain of collagen type IV. A principal structural component of basement membranes | |||||||||
Function / homology | ![]() retinal blood vessel morphogenesis / collagen type IV trimer / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization / extracellular matrix structural constituent conferring tensile strength ...retinal blood vessel morphogenesis / collagen type IV trimer / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Laminin interactions / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / NCAM1 interactions / blood vessel morphogenesis / Scavenging by Class A Receptors / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / neuromuscular junction development / branching involved in blood vessel morphogenesis / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / epithelial cell differentiation / extracellular matrix organization / cellular response to amino acid stimulus / brain development / collagen-containing extracellular matrix / endoplasmic reticulum lumen / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Casino, P. / Marina, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of collagen IV globular domains: insight into associated pathologies, folding and network assembly. Authors: Casino, P. / Gozalbo-Rovira, R. / Rodriguez-Diaz, J. / Banerjee, S. / Boutaud, A. / Rubio, V. / Hudson, B.G. / Saus, J. / Cervera, J. / Marina, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.1 KB | Display | ![]() |
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PDB format | ![]() | 231 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466 KB | Display | ![]() |
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Full document | ![]() | 474.2 KB | Display | |
Data in XML | ![]() | 54.8 KB | Display | |
Data in CIF | ![]() | 77.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5naxC ![]() 5nazC ![]() 5nb0C ![]() 5nb1C ![]() 5nb2C ![]() 1t60S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25356.871 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.4 M lithium sulfate and 0.1 M Mes pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→91.046 Å / Num. all: 142960 / Num. obs: 142960 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.09 / Rsym value: 0.076 / Net I/av σ(I): 7.8 / Net I/σ(I): 10.7 / Num. measured all: 479345 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T60 Resolution: 1.8→57.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.585 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.107 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 58.9 Å2 / Biso mean: 19.085 Å2 / Biso min: 9.82 Å2
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Refinement step | Cycle: final / Resolution: 1.8→57.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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