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Yorodumi- PDB-2ewo: X-ray structure of putative agmatine deiminase Q8DW17, Northeast ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ewo | ||||||
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Title | X-ray structure of putative agmatine deiminase Q8DW17, Northeast Structural Genomics target SmR6. | ||||||
Components | Putative agmatine deiminase | ||||||
Keywords | HYDROLASE / Q8DW17 / SmR6 / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Kuzin, A.P. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: X-ray structure of putative agmatine deiminase Q8DW17, Northeast Structural Genomics target SmR6. Authors: Kuzin, A.P. / Chen, Y. / Vorobiev, S.M. / Su, M. / Forouhar, F. / Acton, T. / Xiao, R. / Conover, K. / Ma, L.-C. / Kellie, R. / Cunningham, K.E. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ewo.cif.gz | 803.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ewo.ent.gz | 696.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ewo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/2ewo ftp://data.pdbj.org/pub/pdb/validation_reports/ew/2ewo | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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-Components
#1: Protein | Mass: 43330.594 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: aguA / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8DW17, agmatine deiminase #2: 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: 2.44 Å3/Da / Density % sol: 49.69 % Description: THE STRUCTURE FACTOR FILE contians FRIEDEL PAIRS. |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: 16% PEG6K, 100mM Tris-HCl, 400mM LiCl, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97938 0.97952 0.96793 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 2005 / Details: mirrors | ||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. obs: 218714 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.1 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 182654.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: The toatal number of unique reflections is 437428. There are 218714 of Friedel pairs. But only 182596 reflections was used for resolution range 20.0A -2.9A, for F > 2sigmaF.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.265542 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 46.7 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: 0.012 / Total num. of bins used: 6
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Xplor file |
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