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Yorodumi- PDB-2imo: Crystal structure of allantoate amidohydrolase from Escherichia c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2imo | ||||||
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Title | Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6 | ||||||
Components | Allantoate amidohydrolase | ||||||
Keywords | HYDROLASE / allantoate amidohydrolase / apoenzyme / allC / T1507 / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information allantoate deiminase / allantoate deiminase activity / allantoin assimilation pathway / purine nucleobase metabolic process / manganese ion binding / protein homodimerization activity / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia coli Reveals its Mechanics. Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2imo.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2imo.ent.gz | 134.4 KB | Display | PDB format |
PDBx/mmJSON format | 2imo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/2imo ftp://data.pdbj.org/pub/pdb/validation_reports/im/2imo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47756.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: allC_ecoli / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P77425, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines #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: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.05 M KH2PO4, 20%PEG8000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9877,0.9792,0.94 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2004 / Details: Mirrors | ||||||||||||
Radiation | Monochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. all: 19631 / Num. obs: 19631 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.9 | ||||||||||||
Reflection shell | Resolution: 2.8→2.88 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 1501 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→48.78 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 105623.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The missing residues listed in Remark 465 are due to lack of or weak electron density.
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Solvent computation | Bsol: 61.0507 Å2 / ksol: 0.399288 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→48.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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Xplor file |
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