[English] 日本語
Yorodumi- PDB-2a2u: THE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a2u | ||||||
---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYALINE DROPLET INDUCER. | ||||||
Components | PROTEIN (ALPHA-2U-GLOBULIN) | ||||||
Keywords | LIPID BINDING PROTEIN / A2U-GLOBULIN | ||||||
Function / homology | Function and homology information positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / energy reserve metabolic process / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / negative regulation of lipid storage ...positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / energy reserve metabolic process / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / negative regulation of lipid storage / heat generation / small molecule binding / locomotor rhythm / negative regulation of gluconeogenesis / mitochondrion organization / aerobic respiration / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chaudhuri, B.N. / Kleywegt, G.J. / Jones, T.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: The structures of alpha 2u-globulin and its complex with a hyaline droplet inducer. Authors: Chaudhuri, B.N. / Kleywegt, G.J. / Bjorkman, J. / Lehman-McKeeman, L.D. / Oliver, J.D. / Jones, T.A. #1: Journal: Adv.Protein Chem. / Year: 1994 Title: Lipid-Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins Authors: Banaszak, L. / Winter, N. / Xu, Z. / Bernlohr, D.A. / Cowan, S.W. / Jones, T.A. #2: Journal: Nature / Year: 1992 Title: Pheromone Binding to Two Rodent Urinary Proteins Revealed by X-Ray Crystallography Authors: Bocskei, Z. / Groom, C.R. / Flower, D.R. / Wright, C.E. / Phillips, S.E.V. / Cavaggioni, A. / Findlay, J.B.C. / North, A.C.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a2u.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a2u.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a2u_validation.pdf.gz | 449.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2a2u_full_validation.pdf.gz | 462.5 KB | Display | |
Data in XML | 2a2u_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 2a2u_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/2a2u ftp://data.pdbj.org/pub/pdb/validation_reports/a2/2a2u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 20764.854 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED FROM MALE RAT URINE / Source: (natural) Rattus norvegicus (Norway rat) / Secretion: URINE / References: UniProt: P02761 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.7 / Details: pH 4.70 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Type: OTHER / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48 Å / Num. obs: 25797 / % possible obs: 95.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.5→2.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.9 / % possible all: 94.6 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 48 Å / Redundancy: 3.1 % / Num. measured all: 78794 |
Reflection shell | *PLUS % possible obs: 94.6 % / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A MONOCLINIC FORM OF A2U (REF 3) Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|