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Yorodumi- PDB-1b8e: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE BOVINE BETA-LACTOGLOBULI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b8e | ||||||
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Title | HIGH RESOLUTION CRYSTAL STRUCTURE OF THE BOVINE BETA-LACTOGLOBULIN (ISOFORMS A AND B) IN ORTHOROMBIC SPACE GROUP | ||||||
Components | PROTEIN (BETA-LACTOGLOBULIN) | ||||||
Keywords | TRANSPORT PROTEIN / BETA-LACTOGLOBULIN / VARIANTS / LIPOCALIN | ||||||
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: 1.95 Å | ||||||
Authors | Oliveira, K.M.G. / Sawyer, L. / Polikarpov, I. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: Crystal structures of bovine beta-lactoglobulin in the orthorhombic space group C222(1). Structural differences between genetic variants A and B and features of the Tanford transition. Authors: Oliveira, K.M. / Valente-Mesquita, V.L. / Botelho, M.M. / Sawyer, L. / Ferreira, S.T. / Polikarpov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b8e.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8e.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 1b8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8e ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8e | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ALL REAGENTS WERE PURCHASED FROM SIGMA / Source: (natural) Bos taurus (cattle) / Organ: BREAST / Secretion: MILK / Variant: VARIANT B / Tissue: MAMMARY GLAND / References: UniProt: P02754 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE VARIANT B DIFFERS IN PRIMARY AMINO ACID SEQUENCE FROM VARIANT A AT THE POSITIONS 64 (GLU-->ASP) ...THE VARIANT B DIFFERS IN PRIMARY AMINO ACID SEQUENCE FROM VARIANT A AT THE POSITIONS 64 (GLU-->ASP) AND 118 (ALA -->VAL) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.9 Details: METHOD IN PRESENCE OF AMMONIUM SULPHATE 2.5 M, 180MM TRIZMA BUFFER AT A PROTEIN CONCENTRATION OF 20MG/ML, pH 7.9, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→14.98 Å / Num. obs: 9834 / % possible obs: 86.4 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 25.18 Å2 / Rsym value: 0.085 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.95→2 Å / Rsym value: 0.44 / % possible all: 88.8 |
Reflection | *PLUS Lowest resolution: 15 Å / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 88.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: B-LG LATTICE Y FROM MIXTURE OF GENETIC VARIANTS A AND B Resolution: 1.95→9.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15
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Displacement parameters | Biso mean: 42.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→9.5 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.256 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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