+Open data
-Basic information
Entry | Database: PDB / ID: 1gt3 | ||||||
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Title | Complex of Bovine Odorant Binding Protein with dihydromyrcenol | ||||||
Components | ODORANT-BINDING PROTEIN | ||||||
Keywords | ODORANT BINDING PROTEIN / LIPOCALIN | ||||||
Function / homology | Function and homology information odorant binding / small molecule binding / sensory perception of smell / extracellular space Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Vincent, F. / Ramoni, R. / Spinelli, S. / Grolli, S. / Conti, V. / Cambillau, C. / Tegoni, M. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2004 Title: Crystal Structures of Bovine Odorant-Binding Protein in Complex with Odorant Molecules. Authors: Vincent, F. / Ramoni, R. / Spinelli, S. / Grolli, S. / Tegoni, M. / Cambillau, C. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gt3.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gt3.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gt3_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
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Full document | 1gt3_full_validation.pdf.gz | 472.5 KB | Display | |
Data in XML | 1gt3_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1gt3_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/1gt3 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/1gt3 | HTTPS FTP |
-Related structure data
Related structure data | 1gt1C 1gt4C 1gt5C 1obpS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 18528.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: DIHYDROMYRCENOL AS LIGAND / Source: (natural) BOS TAURUS (cattle) / Organ: NOSE / Tissue: RESPIRATORY EPITHELIUM / References: UniProt: P07435 #2: Chemical | #3: Chemical | #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: 2.04 Å3/Da / Density % sol: 39.7 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.2 / Details: pH 4.20 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35 Å / Num. obs: 28007 / % possible obs: 80.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 6.4 / % possible all: 80.3 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 35 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OBP Resolution: 1.8→10 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 26271 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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