+Open data
-Basic information
Entry | Database: PDB / ID: 2o8n | ||||||
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Title | Crystal Structure of Mouse Apolipoprotein A-I Binding Protein | ||||||
Components | ApoA-I binding protein | ||||||
Keywords | PROTEIN BINDING / Rossmann fold | ||||||
Function / homology | Function and homology information membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis ...membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis / cilium / cell body / nucleotide binding / mitochondrion / extracellular space / extracellular region / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Shumilin, I.A. / Jha, K.N. / Zheng, H. / Chruszcz, M. / Cymborowski, M. / Herr, J.C. / Minor, W. | ||||||
Citation | Journal: Endocrinology / Year: 2008 Title: Biochemical and Structural Characterization of Apolipoprotein A-I Binding Protein, a Novel Phosphoprotein with a Potential Role in Sperm Capacitation. Authors: Jha, K.N. / Shumilin, I.A. / Digilio, L.C. / Chertihin, O. / Zheng, H. / Schmitz, G. / Visconti, P.E. / Flickinger, C.J. / Minor, W. / Herr, J.C. | ||||||
History |
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Remark 999 | SEQUENCE MSE 0 is an initiating methionine and a modified residue |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o8n.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o8n.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 2o8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/2o8n ftp://data.pdbj.org/pub/pdb/validation_reports/o8/2o8n | 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 on special symmetry positions |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 29872.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apoa1bp, AIBP / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8K4Z3 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CL / |
#4: 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: 3 Å3/Da / Density % sol: 59.01 % |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 0.1 M sodium acetate, 1.5 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 |
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 19, 2005 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2→80.32 Å / Num. obs: 24177 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 56.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 8.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→80.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.043 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2→80.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.06 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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