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- PDB-5sbj: The crystal structure of METP in complex with Cd at a resolution ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5sbj | ||||||
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Title | The crystal structure of METP in complex with Cd at a resolution of 1.29 A. | ||||||
![]() | METP, miniaturized rubredoxin | ||||||
![]() | DE NOVO PROTEIN | ||||||
Function / homology | : ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Di Costanzo, L. / La Gatta, S. / Pavone, V. | ||||||
![]() | ![]() Title: Miniaturization process reloaded - structural and functional insights from a miniaturized rubredoxin Authors: Chino, M. / Di Costanzo, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.8 KB | Display | ![]() |
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PDB format | ![]() | 16.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Group deposition
ID | G_1002191 (3 entries) |
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Title | Structural insights from a miniaturized rubredoxin |
Type | undefined |
Description | Crystal structures of METP in complex with different metals |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 2955.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-CD / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28.37 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 1.4 M sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: CCD / Date: Dec 24, 2020 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.01→31.02 Å / Num. obs: 19836 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.15 % / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.16 / Net I/σ(I): 3.95 |
Reflection shell | Resolution: 1.01→1.07 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.07 / Num. unique obs: 3171 / CC1/2: 0.053 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Rosetta, computational model Resolution: 1.28→31.02 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.61 / Stereochemistry target values: ML
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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 max: 60.34 Å2 / Biso mean: 15.3847 Å2 / Biso min: 8.18 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.28→31.02 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %
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