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Open data
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Basic information
Entry | Database: PDB / ID: 3hvm | ||||||
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Title | Agmatine Deiminase from Helicobacter pylori | ||||||
![]() | AGMATINE DEIMINASE | ||||||
![]() | HYDROLASE / Agmatine Deiminase | ||||||
Function / homology | putrescine biosynthetic process / Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / protein-arginine deiminase activity / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / Putative![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jones, J. / Lovelace, L. / Lebioda, L. / Thompson, P. | ||||||
![]() | ![]() Title: Characterization and inactivation of an agmatine deiminase from Helicobacter pylori. Authors: Jones, J.E. / Causey, C.P. / Lovelace, L. / Knuckley, B. / Flick, H. / Lebioda, L. / Thompson, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.3 KB | Display | ![]() |
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PDB format | ![]() | 60.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cmuS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37614.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | MUTATIONS OCCURRED DURING CLONING OF HPAGD |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 15% PEG 4K, 10 mM sodium citrate pH 5.6, and 7% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2007 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30.37 Å / Num. obs: 18081 / % possible obs: 76 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Χ2: 1.374 / Net I/σ(I): 31.053 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 16.5 / Num. unique all: 1384 / Χ2: 0.82 / % possible all: 59.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2CMU Resolution: 2.1→30.37 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.84 / SU B: 9.861 / SU ML: 0.121 / SU R Cruickshank DPI: 0.374 / SU Rfree: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.246 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.93 Å2 / Biso mean: 29.966 Å2 / Biso min: 8.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.156 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.5798 Å / Origin y: -0.6163 Å / Origin z: -17.9363 Å
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Refinement TLS group |
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