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- PDB-7rgv: Structure of Caulobacter crescentus Suppressor of copper sensitiv... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rgv | ||||||
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Title | Structure of Caulobacter crescentus Suppressor of copper sensitivity protein C | ||||||
![]() | Thioredoxin domain-containing protein | ||||||
![]() | OXIDOREDUCTASE / thioredoxin-like / ScsC / isomerase / periplasmic | ||||||
Function / homology | Copper resistance protein ScsC, N-terminal / Copper resistance protein ScsC N-terminal domain / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / oxidoreductase activity / Thioredoxin domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petit, G.A. / Martin, J.L. / Gulbis, J.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The suppressor of copper sensitivity protein C from Caulobacter crescentus is a trimeric disulfide isomerase that binds copper(I) with subpicomolar affinity. Authors: Petit, G.A. / Hong, Y. / Djoko, K.Y. / Whitten, A.E. / Furlong, E.J. / McCoy, A.J. / Gulbis, J.M. / Totsika, M. / Martin, J.L. / Halili, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.1 KB | Display | ![]() |
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PDB format | ![]() | 109.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.6 KB | Display | ![]() |
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Full document | ![]() | 418.6 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4vxwS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25166.631 Da / Num. of mol.: 1 / Mutation: C2S Source method: isolated from a genetically manipulated source Details: Linker and TEV scar not visible in the electron densities hence not modelled Source: (gene. exp.) ![]() Strain: ATCC 19089 / CB15 / Gene: CC_1879 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65 % / Description: thick hexagonal crystalline rod |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: Protein reduced with DTT and purified in 25 mM HEPES pH 7.5, 150 mM NaCl. Protein concentrated to 130 mg/ml. 1ul of protein solution mixed with 1ul of crystallant solution: 39% MPD, 200 mM ...Details: Protein reduced with DTT and purified in 25 mM HEPES pH 7.5, 150 mM NaCl. Protein concentrated to 130 mg/ml. 1ul of protein solution mixed with 1ul of crystallant solution: 39% MPD, 200 mM NaAcetate, 20 mM CaCl2 pH 7.25 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→49.34 Å / Num. obs: 10854 / % possible obs: 98.75 % / Redundancy: 12 % / Biso Wilson estimate: 90.52 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Rrim(I) all: 0.054 / Net I/σ(I): 22.51 |
Reflection shell | Resolution: 2.63→2.74 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 1045 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.431 / Rrim(I) all: 1.52 / % possible all: 94.76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4VXW res 50-224 chain A Resolution: 2.63→49.34 Å / SU ML: 0.3672 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.1233 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Cycle of automated refinement with Phenix + manual refinemetn with Coot. No real space refinement with Phenix, 2 TLS groups 2-63, 64-223. Secondary structure restraint to keep helices in ...Details: Cycle of automated refinement with Phenix + manual refinemetn with Coot. No real space refinement with Phenix, 2 TLS groups 2-63, 64-223. Secondary structure restraint to keep helices in place. Structure has very few crystal contact+ large solvent channel and is expected to be dynamic hence the very high B-factors
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 122.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.63→49.34 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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