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Yorodumi- PDB-1twi: Crystal structure of Diaminopimelate Decarboxylase from m. jannas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1twi | ||||||
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Title | Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine | ||||||
Components | Diaminopimelate decarboxylase | ||||||
Keywords | LYASE / antibiotic resistance / diaminopimelate decarboxylase / lysine biosynthesis / structural genomics / NYSGXRC / T135 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Rajashankar, K.R. / Ray, S.S. / 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) | ||||||
Citation | Journal: Structure / Year: 2002 Title: Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor Authors: Rajashankar, K.R. / Ray, S.S. / 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1twi.cif.gz | 375.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1twi.ent.gz | 301.8 KB | Display | PDB format |
PDBx/mmJSON format | 1twi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/1twi ftp://data.pdbj.org/pub/pdb/validation_reports/tw/1twi | HTTPS FTP |
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-Related structure data
Related structure data | 1tufSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | Protomers A and B together form one biological assembly and protomers C and D together form a second one. |
-Components
#1: Protein | Mass: 48441.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: LYSA, MJ1097 / Plasmid: PET T7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q58497, diaminopimelate decarboxylase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-LYS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12% PEG6000, 0.1M Tris-HCl, pH 8.0, 20mM MgCl2, 10mM L-lysine, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 4, 2001 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 119738 / Num. obs: 119738 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.035 / Net I/σ(I): 35.37 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 13.06 / Num. unique all: 12081 / Rsym value: 0.101 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TUF Resolution: 2→29.25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 574854.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: There are four molecules in the asymmetric unit. Each has a bound PLP. Molecules A and B have an L-Lysine bound at the active site. Molecules C and D have two L-Lysines near the active site. ...Details: There are four molecules in the asymmetric unit. Each has a bound PLP. Molecules A and B have an L-Lysine bound at the active site. Molecules C and D have two L-Lysines near the active site. One Mg+2 ion is located.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.8907 Å2 / ksol: 0.359056 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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