+Open data
-Basic information
Entry | Database: PDB / ID: 2q2p | ||||||
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Title | Beta-lactoglobulin (reverse native) | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / LIPOCALIN / VARIANT A | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.96 Å | ||||||
Authors | Vijayalakshmi, L. / Krishna, R. / Sankaranarayanan, R. / Vijayan, M. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: An asymmetric dimer of beta-lactoglobulin in a low humidity crystal form-Structural changes that accompany partial dehydration and protein action. Authors: Vijayalakshmi, L. / Krishna, R. / Sankaranarayanan, R. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q2p.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q2p.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 2q2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q2p_validation.pdf.gz | 426.9 KB | Display | wwPDB validaton report |
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Full document | 2q2p_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 2q2p_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 2q2p_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/2q2p ftp://data.pdbj.org/pub/pdb/validation_reports/q2/2q2p | HTTPS FTP |
-Related structure data
Related structure data | 2q2mC 2q39C 1b8eS 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 second part of the biological assembly is generated by the two fold axis: 2-x,y,1/2-z |
-Components
#1: Protein | Mass: 18387.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: VARIANT A DIFFERS IN A PRIMARY AMINO ACID SEQUENCE FROM VARIANT B AT POSITIONS 64 (ASP-->GLY) AND 118 (VAL-->ALA) Source: (natural) Bos taurus (cattle) / Organ: BREAST / Variant: A / Tissue: MAMMARY GLAND / References: UniProt: P02754 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.01M Hepes, 2.2 to 2.8 M Ammonium sulphate, NAOH, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→19.85 Å / Num. obs: 3248 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.96→3.15 Å / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 4.4 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1B8E Resolution: 2.96→19.84 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1020933.96 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0171 Å2 / ksol: 0.22153 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 77.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.96→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.96→3.15 Å / Rfactor Rfree error: 0.065 / Total num. of bins used: 6
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Xplor file |
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