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Open data
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Basic information
Entry | Database: PDB / ID: 1jra | ||||||
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Title | Crystal Structure of Erv2p | ||||||
![]() | ERV2 PROTEIN, MITOCHONDRIAL | ||||||
![]() | OXIDOREDUCTASE / FAD / sulfhydryl oxidase / helical bundle / CXXC | ||||||
Function / homology | ![]() flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / fungal-type vacuole / fungal-type vacuole membrane / flavin adenine dinucleotide binding / endoplasmic reticulum membrane / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gross, E. / Sevier, C.S. / Vala, A. / Kaiser, C.A. / Fass, D. | ||||||
![]() | ![]() Title: A new FAD-binding fold and intersubunit disulfide shuttle in the thiol oxidase Erv2p. Authors: Gross, E. / Sevier, C.S. / Vala, A. / Kaiser, C.A. / Fass, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.4 KB | Display | ![]() |
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PDB format | ![]() | 84 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jr8SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer. The asymmetric unit contains two dimers. |
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Components
#1: Protein | Mass: 13524.354 Da / Num. of mol.: 4 / Fragment: protease-resistant domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ERV2 / Plasmid: pAED4 / Production host: ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.44 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 8000, sodium cacodylate, magnesium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 21, 2000 / Details: osmic mirrors |
Radiation | Monochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 28911 / Num. obs: 28807 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2869 / % possible all: 98.3 |
Reflection | *PLUS % possible obs: 99.8 % |
Reflection shell | *PLUS % possible obs: 98.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1JR8 prior to refinement Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection obs: 26812 / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |