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- PDB-1xkn: Crystal Structure of the Putative Peptidyl-arginine Deiminase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xkn | ||||||
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Title | Crystal Structure of the Putative Peptidyl-arginine Deiminase from Chlorobium tepidum, NESG Target CtR21 | ||||||
![]() | putative peptidyl-arginine deiminase | ||||||
![]() | STRUCTURAL GENOMICS / alpha-beta protein / NESG / Protein Structure Initiative / PSI / Northeast Structural Genomics Consortium | ||||||
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 / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Befeler, A.R. / Vorobiev, S.M. / Hussain, M. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal Structure of the Putative Peptidyl-arginine Deiminase from Chlorobium tepidum, NESG Target CtR21 Authors: Forouhar, F. / Befeler, A.R. / Vorobiev, S.M. / Hussain, M. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.9 KB | Display | ![]() |
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PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368.9 KB | Display | ![]() |
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Full document | ![]() | 372.2 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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: 40681.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100 mM Na3Citrate (pH 5.6), 18% PEG8K, 50 mM KH2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.62 Å / Num. all: 84665 / Num. obs: 83239 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.75 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.073 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 8.2 / Num. unique all: 8855 / Rsym value: 0.268 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.8357 Å2 / ksol: 0.309323 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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