+Open data
-Basic information
Entry | Database: PDB / ID: 2dg2 | ||||||
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Title | Crystal Structure of Mouse Apolipoprotein A-I Binding Protein | ||||||
Components | Apolipoprotein A-I binding protein | ||||||
Keywords | PROTEIN BINDING / Disordered N-terminus | ||||||
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: 2.45 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dg2.cif.gz | 277.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dg2.ent.gz | 235.1 KB | Display | PDB format |
PDBx/mmJSON format | 2dg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/2dg2 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/2dg2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg label comp-ID: VAL / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 27 - 258 / Label seq-ID: 28 - 259
NCS ensembles :
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Details | The biological assembly is a dimer, three of which are present in the asymmetric unit |
-Components
#1: Protein | Mass: 29826.068 Da / Num. of mol.: 6 / Fragment: residues 0-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apoa1bp / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 37231544, UniProt: Q8K4Z3*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.5M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97898 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 15, 2005 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97898 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→80 Å / Num. all: 69794 / Num. obs: 69794 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→80 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 16.524 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.229 / 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: 40.881 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→80 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 3467 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 23.3848 Å / Origin y: 39.4476 Å / Origin z: 38.6855 Å
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