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Yorodumi- PDB-2a2g: THE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a2g | ||||||
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Title | THE CRYSTAL STRUCTURES OF A2U-GLOBULIN AND ITS COMPLEX WITH A HYALINE DROPLET INDUCER. | ||||||
Components | PROTEIN (ALPHA-2U-GLOBULIN) | ||||||
Keywords | LIPID BINDING PROTEIN / LIPID-BINDING PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / cellular response to lipid / 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 / heat generation ...positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / cellular response to lipid / 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 / heat generation / small molecule binding / locomotor rhythm / negative regulation of lipid storage / negative regulation of gluconeogenesis / aerobic respiration / mitochondrion organization / 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: 2.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a2g.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a2g.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 2a2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a2g_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 2a2g_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 2a2g_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2a2g_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/2a2g ftp://data.pdbj.org/pub/pdb/validation_reports/a2/2a2g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-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: Chemical | ChemComp-LEO / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.8 / Details: pH 4.80 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49 Å / Num. obs: 15350 / % possible obs: 88 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.6 / % possible all: 91.3 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 49 Å / Redundancy: 3.2 % / Num. measured all: 49636 |
Reflection shell | *PLUS % possible obs: 91.3 % / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AN ORTHORHOMBIC FORM OF A2U Resolution: 2.9→10 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE LIGAND WAS *NOT* INCLUDED IN THE REFINEMENT
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.398 / Rfactor Rwork: 0.321 |