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Yorodumi- PDB-1gxa: BOVINE BETA-LACTOGLOBULIN COMPLEXED WITH RETINOL AND PALMITIC ACI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gxa | ||||||
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Title | BOVINE BETA-LACTOGLOBULIN COMPLEXED WITH RETINOL AND PALMITIC ACID, TRIGONAL LATTICE Z | ||||||
Components | BETA-LACTOGLOBULIN | ||||||
Keywords | LIPOCALIN / MILK / WHEY TRANSPORT / BOVINE / PALMITIC ACID-BINDI ALLERGEN | ||||||
Function / homology | Function and homology information retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Kontopidis, G. / Sawyer, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The Ligand-Binding Site of Bovine Beta-Lactoglobulin: Evidence for a Function? Authors: Kontopidis, G. / Holt, C. / Sawyer, L. #1: Journal: J.Biol.Chem. / Year: 1999 Title: Beta-Lactoglobuli Binds Palmitate within its Central Cavity Authors: Wu, S.-Y. / Perez, M.D. / Puyol, P. / Sawyer, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gxa.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gxa.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gxa ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gxa | HTTPS FTP |
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-Related structure data
Related structure data | 1gx8C 1gx9C 1b0oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE DIMER GIVEN HERE IS PHYSIOLOGICAL DIMERTHE STRAND AA10 CREATES A CONTINUOUS BETA SHEET BETWEENRESIDUES 147-150 IN THE DIMER |
-Components
#1: Protein | Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: PROTEIN PURCHASED FROM SIGMA CHEMICALS, CAT.NO. L8005 Source: (natural) BOS TAURUS (cattle) / Organ: MAMMARY GLAND / Variant: GENETIC VARIANT B / References: UniProt: P02754 |
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#2: Chemical | ChemComp-PLM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.495 Å3/Da / Density % sol: 51.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / pH: 7.3 Details: 17 DEG C, 8MUL BLG-RET-PLM COMPLEX 20MM TRIS, PH 8 + 8MUL NA CITRATE 1.25M, 0.1M HEPES, PH7.3, PER DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.3 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: SILICON |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→25 Å / Num. obs: 8186 / % possible obs: 99.2 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.2 |
Reflection shell | Rmerge(I) obs: 0.254 / % possible all: 97.2 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 123391 |
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B0O Resolution: 2.35→25 Å / Num. parameters: 5542 / Num. restraintsaints: 5306 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: THE RESIDUE, LEU 1 IS NOT OBSERVED
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1411.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→25 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.226 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |