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Yorodumi- PDB-1pz4: The structural determination of an insect (mosquito) Sterol Carri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pz4 | ||||||
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Title | The structural determination of an insect (mosquito) Sterol Carrier Protein-2 with a ligand bound C16 Fatty Acid at 1.35 A resolution | ||||||
Components | sterol carrier protein 2 | ||||||
Keywords | LIPID BINDING PROTEIN / alpha and beta | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aedes aegypti (yellow fever mosquito) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Dyer, D.H. / Lovell, S. / Thoden, J.B. / Holden, H.M. / Rayment, I. / Lan, Q. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The Structural Determination of an Insect Sterol Carrier Protein-2 with a Ligand-bound C16 Fatty Acid at 1.35A Resolution Authors: Dyer, D.H. / Lovell, S. / Thoden, J.B. / Holden, H.M. / Rayment, I. / Lan, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pz4.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pz4.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pz4_validation.pdf.gz | 612.9 KB | Display | wwPDB validaton report |
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Full document | 1pz4_full_validation.pdf.gz | 614.7 KB | Display | |
Data in XML | 1pz4_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1pz4_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pz4 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pz4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12855.876 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86PR3 |
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#2: Chemical | ChemComp-PLM / |
#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: 1.85 Å3/Da / Density % sol: 33.46 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M sodium malonate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
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: 1.54178 / Wavelength: 1.54178 Å |
Detector | Type: Bruker X1000 / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→100 Å / Num. all: 21157 / Num. obs: 21157 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.35→1.41 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2383 / % possible all: 92 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 97 % / Num. measured all: 78412 |
Reflection shell | *PLUS % possible obs: 91.5 % / Num. unique obs: 2383 / Num. measured obs: 5542 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.35→100 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rwork: 0.184 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 1.41 Å / Num. reflection Rfree: 2107 / Num. reflection Rwork: 19050 / Num. reflection obs: 21157 |