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Open data
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Basic information
Entry | Database: PDB / ID: 1h4u | ||||||
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Title | Domain G2 of mouse nidogen-1 | ||||||
![]() | NIDOGEN-1 | ||||||
![]() | EXTRACELLULAR MATRIX PROTEIN | ||||||
Function / homology | ![]() Laminin interactions / regulation of basement membrane organization / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / Degradation of the extracellular matrix / Wnt receptor activity / Wnt-protein binding / protein complex involved in cell-matrix adhesion / extracellular matrix binding ...Laminin interactions / regulation of basement membrane organization / glomerular basement membrane development / laminin-1 binding / positive regulation of integrin-mediated signaling pathway / Degradation of the extracellular matrix / Wnt receptor activity / Wnt-protein binding / protein complex involved in cell-matrix adhesion / extracellular matrix binding / positive regulation of cell-substrate adhesion / proteoglycan binding / positive regulation of muscle cell differentiation / positive regulation of cell adhesion / basement membrane / canonical Wnt signaling pathway / collagen binding / extracellular matrix organization / cell-matrix adhesion / extracellular matrix / cell periphery / collagen-containing extracellular matrix / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hopf, M. / Gohring, W. / Ries, A. / Timpl, R. / Hohenester, E. | ||||||
![]() | ![]() Title: Crystal Structure and Mutational Analysis of a Perlecan-Binding Fragment of Nidogen-1 Authors: Hopf, M. / Gohring, W. / Ries, A. / Timpl, R. / Hohenester, E. #1: Journal: Embo J. / Year: 1991 Title: Recombinant Nidogen Consists of Three Globular Domains and Mediates Binding of Laminin to Collagen Type Iv Authors: Fox, J.W. / Mayer, U. / Nischt, R. / Aumailley, M. / Reinhardt, D. / Wiedemann, H. / Mann, K. / Timpl, R. / Krieg, T. / Engel, J. / Chu, M.-L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.7 KB | Display | ![]() |
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PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.8 KB | Display | ![]() |
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Full document | ![]() | 428.2 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 29272.756 Da / Num. of mol.: 1 / Fragment: G2 FRAGMENT, RESIDUES 395-659 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.89 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 10 MG/ML PROTEIN, 5-8% PEG4000, 0.1 M ACETATE PH 5.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: QUANTUM4 / Detector: CCD / Date: Aug 18, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 17203 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 15 Å |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |