+Open data
-Basic information
Entry | Database: PDB / ID: 3rgg | ||||||
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Title | Crystal structure of Treponema denticola PurE bound to AIR | ||||||
Components | Phosphoribosylaminoimidazole carboxylase, PurE protein | ||||||
Keywords | LYASE / Purine biosynthesis / Carboxylase | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process Similarity search - Function | ||||||
Biological species | Treponema denticola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Mathews, I.I. / Starks, C.M. / Kappock, T.J. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Treponema denticola PurE Is a Bacterial AIR Carboxylase. Authors: Tranchimand, S. / Starks, C.M. / Mathews, I.I. / Hockings, S.C. / Kappock, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rgg.cif.gz | 258.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rgg.ent.gz | 212.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/3rgg ftp://data.pdbj.org/pub/pdb/validation_reports/rg/3rgg | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17261.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema denticola (bacteria) / Gene: PurE, TDE_0687 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q73PV9, phosphoribosylaminoimidazole carboxylase #2: Chemical | ChemComp-AIR / #3: 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: 2.09 Å3/Da / Density % sol: 41.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14-16% (W/V) PEG 1000, 0.1 M MAGNESIUM CHLORIDE, 0.1 M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 111 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→37.1 Å / Num. all: 51257 / Num. obs: 51257 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.064 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3520 / Rsym value: 0.865 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native coordinate Resolution: 1.82→37.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.459 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.749 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→37.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.869 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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