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Yorodumi- PDB-2hzq: Crystal structure of human apolipoprotein D (ApoD) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hzq | ||||||
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Title | Crystal structure of human apolipoprotein D (ApoD) in complex with progesterone | ||||||
Components | Apolipoprotein D | ||||||
Keywords | TRANSPORT PROTEIN / lipocalin / beta barrel / bilin-binding protein | ||||||
Function / homology | Function and homology information negative regulation of lipoprotein lipid oxidation / negative regulation of T cell migration / Transport of fatty acids / negative regulation of smooth muscle cell-matrix adhesion / peripheral nervous system axon regeneration / negative regulation of focal adhesion assembly / tissue regeneration / lipid transporter activity / negative regulation of monocyte chemotactic protein-1 production / negative regulation of platelet-derived growth factor receptor signaling pathway ...negative regulation of lipoprotein lipid oxidation / negative regulation of T cell migration / Transport of fatty acids / negative regulation of smooth muscle cell-matrix adhesion / peripheral nervous system axon regeneration / negative regulation of focal adhesion assembly / tissue regeneration / lipid transporter activity / negative regulation of monocyte chemotactic protein-1 production / negative regulation of platelet-derived growth factor receptor signaling pathway / cholesterol binding / negative regulation of protein import into nucleus / response to axon injury / negative regulation of cytokine production involved in inflammatory response / cytosolic ribosome / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to reactive oxygen species / negative regulation of smooth muscle cell proliferation / brain development / lipid metabolic process / glucose metabolic process / angiogenesis / neuronal cell body / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Eichinger, A. / Skerra, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural insight into the dual ligand specificity and mode of high density lipoprotein association of apolipoprotein d. Authors: Eichinger, A. / Nasreen, A. / Kim, H.J. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hzq.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hzq.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/2hzq ftp://data.pdbj.org/pub/pdb/validation_reports/hz/2hzq | 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: 19988.102 Da / Num. of mol.: 1 / Mutation: L23P, W99H, C116S, I118S, L120S, P133V, N134A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOD / Plasmid: pApoD27delta(QA) / Production host: Escherichia coli (E. coli) / Strain (production host): KS272 / References: UniProt: P05090 |
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#2: Chemical | ChemComp-STR / |
#3: 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: 2.16 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.1 M lithium sulfate, 0.1 M ammonium formate, 0.075 M Hepes/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0089 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2006 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0089 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.575 Å / Num. all: 17254 / Num. obs: 17084 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: Model of uncomplexed ApoD Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.714 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: Engh & Huber / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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