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- PDB-2qqd: N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qqd | |||||||||
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Title | N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii | |||||||||
![]() | (Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) ...) x 3 | |||||||||
![]() | LYASE / arginine decarboxylase / pyruvoyl / decarboxylation / autoprocessing / serinolysis / Pyruvate | |||||||||
Function / homology | ![]() arginine decarboxylase / arginine decarboxylase activity / arginine catabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ealick, S.E. / Soriano, E.S. | |||||||||
![]() | ![]() Title: Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii. Authors: Soriano, E.V. / McCloskey, D.E. / Kinsland, C. / Pegg, A.E. / Ealick, S.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190 KB | Display | ![]() |
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PDB format | ![]() | 150.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 526.2 KB | Display | ![]() |
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Full document | ![]() | 542 KB | Display | |
Data in XML | ![]() | 39 KB | Display | |
Data in CIF | ![]() | 54.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qqcC ![]() 1n13S C: citing same article ( 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Pyruvoyl-dependent arginine decarboxylase (EC 4.1.1.19) ... , 3 types, 8 molecules ADBECFGH
#1: Protein | Mass: 5523.238 Da / Num. of mol.: 2 / Fragment: Beta subunit / Mutation: N47A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pdaD / Production host: ![]() ![]() #2: Protein | Mass: 12227.369 Da / Num. of mol.: 2 / Fragment: Alpha subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pdaD / Production host: ![]() ![]() #3: Protein | Mass: 17819.684 Da / Num. of mol.: 4 / Mutation: N47A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pdaD / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 341 molecules ![](data/chem/img/AG2.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 17-20% PEG 2000, 10% MPD, 2.5% glycerol, 0.1 M HEPES, 0.005 M beta-octylglucoside, 0.005 M EDTA, 0.010 M DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.13 Å / Num. all: 58029 / Num. obs: 56234 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 2.9 % / Rsym value: 0.04 / % possible all: 83.3 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1N13 Resolution: 2→46.13 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 371512.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.9666 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→46.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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