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Yorodumi- PDB-8c68: CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c68 | |||||||||
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Title | CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAMBIAE (AGAMOBP4) AT PH 4.6 | |||||||||
Components | AGAP010489-PA | |||||||||
Keywords | TRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction | |||||||||
Function / homology | Function and homology information dibutyl phthalate binding / olfactory behavior / odorant binding / sensory perception of smell / extracellular region Similarity search - Function | |||||||||
Biological species | Anopheles gambiae (African malaria mosquito) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Tsitsanou, K.E. / Drakou, C.E. / Zographos, S.E. | |||||||||
Funding support | Greece, 2items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 Title: Influence of pH on indole-dependent heterodimeric interactions between Anopheles gambiae odorant-binding proteins OBP1 and OBP4. Authors: Mam, B. / Tsitsanou, K.E. / Liggri, P.G.V. / Saitta, F. / Stamati, E.C.V. / Mahita, J. / Leonis, G. / Drakou, C.E. / Papadopoulos, M. / Arnaud, P. / Offmann, B. / Fessas, D. / Sowdhamini, R. / Zographos, S.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c68.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c68.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/8c68 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/8c68 | HTTPS FTP |
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-Related structure data
Related structure data | 8c6eC 3n88 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14048.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: OBP-4, 1275228, AgamOBP4, OBP4, AgaP_AGAP010489, agCG48601 Plasmid: PET-22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB(DE3) / References: UniProt: Q8T6R7 | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 4.6 Details: 2.0 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2009 / Details: MULTILAYER MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03796 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→44.86 Å / Num. obs: 8929 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6 / Num. unique obs: 1270 / CC1/2: 0.942 / Rpim(I) all: 0.13 / Rrim(I) all: 0.384 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N88 3n88 Resolution: 2.05→44.86 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.67 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.162 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→44.86 Å
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Refine LS restraints |
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