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- PDB-1tuf: Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tuf | |||||||||
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Title | Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi | |||||||||
![]() | Diaminopimelate decarboxylase | |||||||||
![]() | LYASE / antibiotic resistance / diamnopimilate decarboxylase / lysine biosynthesis / structural genomics / NYSGXRC / T135 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | |||||||||
Function / homology | ![]() diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rajashankar, K. / Ray, S.R. / Bonanno, J.B. / Pinho, M.G. / He, G. / De Lencastre, H. / Tomasz, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | |||||||||
![]() | ![]() Title: Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor Authors: Rajashankar, K. / Ray, S.R. / Bonanno, J.B. / Pinho, M.G. / He, G. / De Lencastre, H. / Tomasz, A. / Burley, S.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 | ![]() | 186.6 KB | Display | ![]() |
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PDB format | ![]() | 146.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.2 KB | Display | ![]() |
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Full document | ![]() | 482.4 KB | Display | |
Data in XML | ![]() | 38.3 KB | Display | |
Data in CIF | ![]() | 52.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 | Protomers A and B together form the biological assembly. |
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Components
#1: Protein | Mass: 48686.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LYSA, MJ1097 / Plasmid: PET T7 / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12% PEG6000, 0.1M Tris-HCl, 20mM MgCl2, 25mM azelaic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.4→30 Å / Num. all: 36391 / Num. obs: 36391 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.077 / Net I/σ(I): 4.9 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.46 Å / Mean I/σ(I) obs: 4.8 / Num. unique all: 1404 / Rsym value: 0.292 / % possible all: 53.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Model built with electron density map calculated using a Platinum derivative. Resolution: 2.4→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 493146.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Data is complete to 2.6A. 2.6 to 2.4 shell is less complete (~60%), however this data was used in refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.6865 Å2 / ksol: 0.350701 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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