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Yorodumi- PDB-1dzk: Porcine Odorant Binding Protein Complexed with pyrazine (2-isobut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dzk | ||||||
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Title | Porcine Odorant Binding Protein Complexed with pyrazine (2-isobutyl-3-metoxypyrazine) | ||||||
Components | ODORANT-BINDING PROTEIN | ||||||
Keywords | TRANSPORT / LIPOCALIN / OLFACTION / SENSORY TRANSDUCTION | ||||||
Function / homology | Function and homology information odorant binding / small molecule binding / sensory perception of smell / extracellular space Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.48 Å | ||||||
Authors | Vincent, F. / Spinelli, S. / Cambillau, C. / Tegoni, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Complexes of Porcine Odorant Binding Protein with Odorant Molecules Belonging to Different Chemical Classes Authors: Vincent, F. / Spinelli, S. / Ramoni, R. / Grolli, S. / Pelosi, P. / Cambillau, C. / Tegoni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dzk.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dzk.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dzk_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 1dzk_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 1dzk_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1dzk_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/1dzk ftp://data.pdbj.org/pub/pdb/validation_reports/dz/1dzk | HTTPS FTP |
-Related structure data
Related structure data | 1dzjC 1dzmC 1dzpC 1e00C 1e02C 1e06C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.15526, 0.00223, -0.98787), Vector: |
-Components
#1: Protein | Mass: 17721.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: NOSE / Tissue: OLFACTORY EPITHELIUM / References: UniProt: P81245 #2: Chemical | #3: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.46 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: PROTEIN (0.47MM) IS INCUBATED WITH 10MM OF PYRAZINE., pH 7.80 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9465 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9465 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→25 Å / Num. obs: 56300 / % possible obs: 92.6 % / Redundancy: 2.72 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.056 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.45 / % possible all: 92.3 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 92.3 % / Rmerge(I) obs: 0.093 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.48→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1300053.96 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: N-TERMINUS FROM RESIDUE 1 - 9, IN SUBUNIT A AND B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES 19A, 39A, 57A, 79A, ...Details: N-TERMINUS FROM RESIDUE 1 - 9, IN SUBUNIT A AND B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES 19A, 39A, 57A, 79A, 98A, 114A, 129A, 133A, 147A, 19B, 52B, 53B, 77B, 89B, 114B, 143B. THE ATOMS CONCERNED HAVE OCCUPANCY BETWEEN 0.0 AND 1.0 AND A SEGID AC1 AND AC2 OFTEN, OCCUPANCY VALUES LOWER THAN 1.0 APPEARED TO JUSTIFY BETTER THE ELECTRON DENSITY. FOR THIS REASON WE HAVE KEPT THIS LOW OCCUPANCY FOR SEVERAL SIDE CHAIN ATOMS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 90.17 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.48→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.56 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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