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Yorodumi- PDB-4jrb: Structure of Cockroach Allergen Bla g 1 Tandem Repeat as a EGFP fusion -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jrb | ||||||
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Title | Structure of Cockroach Allergen Bla g 1 Tandem Repeat as a EGFP fusion | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LIPID BINDING PROTEIN / Allergen / asthma / new fold / proposed lipid binding protein | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) Blattella germanica (German cockroach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.414 Å | ||||||
Authors | Mueller, G.A. / Pedersen, L.C. / Lih, F.B. / Glesner, J. / Moon, A.F. / Chapman, M.D. / Tomer, K. / London, R.E. | ||||||
Citation | Journal: J.Allergy Clin.Immunol. / Year: 2013 Title: The novel structure of the cockroach allergen Bla g 1 has implications for allergenicity and exposure assessment. Authors: Mueller, G.A. / Pedersen, L.C. / Lih, F.B. / Glesner, J. / Moon, A.F. / Chapman, M.D. / Tomer, K.B. / London, R.E. / Pomes, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jrb.cif.gz | 178.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jrb.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jrb_validation.pdf.gz | 700 KB | Display | wwPDB validaton report |
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Full document | 4jrb_full_validation.pdf.gz | 705.2 KB | Display | |
Data in XML | 4jrb_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 4jrb_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jrb ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jrb | HTTPS FTP |
-Related structure data
Related structure data | 3ai4S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46738.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: designed off of pET28a to include a 6HIS-EGFP fusion at the N-terminus with a AAA linker region in between the EGFP and the Blag1 Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Blattella germanica (German cockroach) Gene: GFP / Plasmid: pEGFPX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3-RIL / References: UniProt: P42212, UniProt: Q9UAM5 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-PGT / ( | #4: Chemical | ChemComp-D12 / #5: Water | ChemComp-HOH / | Nonpolymer details | THE LIGAND DENOTED ADS D12 IS AN UNKNOWN FATTY ACID, WITH THE CLOSEST MATCH ON OBSERVED ATOMS TO ...THE LIGAND DENOTED ADS D12 IS AN UNKNOWN FATTY ACID, WITH THE CLOSEST MATCH ON OBSERVED ATOMS TO DODECANE. THE LIGAND DENOTED AS PGT IS AN UNKNOWN PHOSPHOLIP | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM Tris, 10% propanol, 20% PEG4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2012 |
Radiation | Monochromator: si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 23505 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1087 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AI4 Resolution: 2.414→25.188 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.53 Å2 / ksol: 0.308 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.414→25.188 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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