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- PDB-2dgd: Crystal structure of ST0656, a function unknown protein from Sulf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dgd | ||||||
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Title | Crystal structure of ST0656, a function unknown protein from Sulfolobus tokodaii | ||||||
![]() | 223aa long hypothetical arylmalonate decarboxylase | ||||||
![]() | LYASE / OCTAMER / alpha/beta structure | ||||||
Function / homology | Maleate isomerase/Arylmalonate decarboxylase / Arylmalonate decarboxylase / Rossmann fold - #1860 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanaka, Y. / Sasaki, T. / Tanabe, E. / Yao, M. / Tanaka, I. / Kumagai, I. / Tsumoto, K. | ||||||
![]() | ![]() Title: Crystal structure of ST0656, a function unknown protein from Sulfolobus tokodaii Authors: Tanaka, Y. / Sasaki, T. / Tanabe, E. / Yao, M. / Tanaka, I. / Kumagai, I. / Tsumoto, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.9 KB | Display | ![]() |
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PDB format | ![]() | 154.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.2 KB | Display | ![]() |
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Full document | ![]() | 490.9 KB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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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Details | The biological assembly is a octamer generated from the tetramer in the asymmetric unit by the operations: x-y+1, -y+2, -z+2/3. |
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Components
#1: Protein | Mass: 25770.967 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 15621661, UniProt: Q974K3*PLUS, arylmalonate decarboxylase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 0.6M NaCl, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. obs: 31282 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 78.4 Å2 / Rsym value: 0.094 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 9 % / Num. unique all: 3052 / Rsym value: 0.429 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.3099 Å2 / ksol: 0.354468 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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