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Open data
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Basic information
Entry | Database: PDB / ID: 1ck4 | ||||||
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Title | CRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN. | ||||||
![]() | INTEGRIN ALPHA-1 | ||||||
![]() | STRUCTURAL PROTEIN / I-DOMAIN / METAL BINDING / COLLAGEN / ADHESION | ||||||
Function / homology | ![]() Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity ...Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity / collagen binding / neutrophil chemotaxis / cell-matrix adhesion / neuron projection morphogenesis / cell chemotaxis / acrosomal vesicle / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / positive regulation of neuron apoptotic process / integrin binding / perikaryon / protein phosphatase binding / positive regulation of MAPK cascade / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / signaling receptor binding / cell surface / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nolte, M. / Pepinsky, R.B. / Venyaminov, S.Y. / Koteliansky, V. / Gotwals, P.J. / Karpusas, M. | ||||||
![]() | ![]() Title: Crystal structure of the alpha1beta1 integrin I-domain: insights into integrin I-domain function. Authors: Nolte, M. / Pepinsky, R.B. / Venyaminov, S.Y.u. / Koteliansky, V. / Gotwals, P.J. / Karpusas, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.9 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.3 KB | Display | ![]() |
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Full document | ![]() | 455.8 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aoxS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99929, 0.00081, 0.03763), Vector: |
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Components
#1: Protein | Mass: 22118.053 Da / Num. of mol.: 2 / Fragment: I-DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.22 Å3/Da / Density % sol: 45.03 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. obs: 19238 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 77.6 % / Mean I/σ(I) obs: 3.14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AOX Resolution: 2.2→100 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: FOR CHAIN A, SIDE CHAINS OF RESIDUES 145, 146, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS. FOR CHAIN B, SIDE CHAINS OF RESIDUES 145, 175, 234 ARE ...Details: FOR CHAIN A, SIDE CHAINS OF RESIDUES 145, 146, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS. FOR CHAIN B, SIDE CHAINS OF RESIDUES 145, 175, 234 ARE ASSIGNED 0.0 OCCUPANCY DUE TO ABSENCE OF ELECTRON DENSITY FOR THE SIDE CHAINS.
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Refinement step | Cycle: LAST / Resolution: 2.2→100 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.6 |