[English] 日本語
![](img/lk-miru.gif)
- PDB-4mvk: Crystal structure of an engineered lipocalin (Anticalin US7) in c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4mvk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide fragment VFFAED | ||||||
![]() |
| ||||||
![]() | PROTEIN BINDING/PROTEIN FIBRIL / ![]() ![]() | ||||||
Function / homology | ![]() siderophore transport / Metal sequestration by antimicrobial proteins / regulation of epidermal growth factor-activated receptor activity / iron ion sequestering activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands ...siderophore transport / Metal sequestration by antimicrobial proteins / regulation of epidermal growth factor-activated receptor activity / iron ion sequestering activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Eichinger, A. / Skerra, A. | ||||||
![]() | ![]() Title: High-affinity Anticalins with aggregation-blocking activity directed against the Alzheimer beta-amyloid peptide. Authors: Rauth, S. / Hinz, D. / Borger, M. / Uhrig, M. / Mayhaus, M. / Riemenschneider, M. / Skerra, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 90.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 67.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4mviC ![]() 4mvlC ![]() 1l6mS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21533.420 Da / Num. of mol.: 1 / Fragment: UNP residues 21-198 Mutation: Q28H,L36V,A40K,I41S,Q49W,L70G,R72G,K73T,D77H,W79K,C87S,N96R,Y100R,L103R,Y106A,K125V,S127Q,Y132S,K134N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: engineered variant US7, HNL, LCN2, LCN2 (NGAL_HUMAN), NGAL Plasmid: pNGAL98-US7 / Production host: ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 750.819 Da / Num. of mol.: 1 / Fragment: UNP residues 689-694 / Source method: obtained synthetically Details: The Abeta hexapeptide fragment VFFAED was synthesized with an acetylated N- and an amidated C-terminus. Source: (synth.) ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.69 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 27 % (w/v) PEG 8000, 100 mM MES, pH 6.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2010 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→42.571 Å / Num. all: 30318 / Num. obs: 30318 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.078 / Net I/σ(I): 13.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing![]() | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1L6M Resolution: 1.5→42.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1959 / WRfactor Rwork: 0.1728 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9001 / SU B: 2.254 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0677 / SU Rfree: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.46 Å2 / Biso mean: 24.3619 Å2 / Biso min: 8.45 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→42.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|