+
Open data
-
Basic information
Entry | Database: PDB / ID: 1t7v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Zn-alpha-2-glycoprotein; baculo-ZAG PEG 200 | |||||||||
![]() | Zinc-alpha-2-glycoprotein | |||||||||
![]() | LIPID BINDING PROTEIN / MHC class I homolog / PEG | |||||||||
Function / homology | ![]() Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / protein transmembrane transporter activity / RNA nuclease activity / collagen-containing extracellular matrix / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space ...Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / protein transmembrane transporter activity / RNA nuclease activity / collagen-containing extracellular matrix / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Delker, S.L. / West Jr., A.P. / McDermott, L. / Kennedy, M.W. / Bjorkman, P.J. | |||||||||
![]() | ![]() Title: Crystallographic studies of ligand binding by Zn-alpha2-glycoprotein. Authors: Delker, S.L. / West Jr., A.P. / McDermott, L. / Kennedy, M.W. / Bjorkman, P.J. #1: ![]() Title: Crystal structure of human ZAG, a fat-depleting factor related to MHC molecules Authors: Sanchez, L.M. / Chirino, A.J. / Bjorkman, P. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1t7wC ![]() 1t7xC ![]() 1t7yC ![]() 1t7zC ![]() 1t80C ![]() 1zagS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 32185.953 Da / Num. of mol.: 1 / Mutation: N89K, N92T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-P6G / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.84 % |
---|---|
Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7.5 Details: Ammonium sulfate, PEG 200, HEPES, pH 7.5, Microbatch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2003 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 36424 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.95→2.02 Å / % possible obs: 98.9 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZAG Resolution: 1.95→20 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 63.5282 Å2 / ksol: 0.378422 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.61 Å2 / Biso mean: 46.52 Å2 / Biso min: 15.48 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|