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- PDB-6m4y: Structure of a R371A mutant of a Group II PLP dependent decarboxy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m4y | ||||||
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Title | Structure of a R371A mutant of a Group II PLP dependent decarboxylase from Methanocaldococcus jannaschii | ||||||
![]() | L-tyrosine/L-aspartate decarboxylase | ||||||
![]() | LYASE / PLP dependent decarboxylase / Catalytic mutant / Protein Conformation / LLP / internal aldimine / Tyrosine / Tyrosine Decarboxylase / Structure-Activity Relationship | ||||||
Function / homology | ![]() methanofuran biosynthetic process / tyrosine decarboxylase / tyrosine decarboxylase activity / sphinganine-1-phosphate aldolase activity / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / sphingolipid catabolic process / carboxylic acid metabolic process / coenzyme A biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Manoj, N. / Chellam Gayathri, S. | ||||||
![]() | ![]() Title: Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases. Authors: Gayathri, S.C. / Manoj, N. #1: ![]() Title: Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. Authors: Chellam Gayathri, S. / Manoj, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.4 KB | Display | ![]() |
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PDB format | ![]() | 125.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.7 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jy1S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 47572.715 Da / Num. of mol.: 1 / Mutation: R371A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: mfnA, MJ0050 / Plasmid: pSpeedET / Details (production host): Bacterial expression vector / Production host: ![]() ![]() References: UniProt: Q60358, aspartate 1-decarboxylase, tyrosine decarboxylase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium citrate pH 5.4, 0.2M sodium potassium tartarate, 2.0M ammonium sulphate PH range: 5.4-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 2017 |
Radiation | Monochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.27 Å / Num. obs: 35618 / % possible obs: 100 % / Redundancy: 26.5 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.041 / Rrim(I) all: 0.212 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 25.9 % / Rmerge(I) obs: 1.202 / Num. unique obs: 2856 / CC1/2: 0.851 / Rpim(I) all: 0.24 / Rrim(I) all: 1.226 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JY1 Resolution: 2.1→38.27 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 92.09 Å2 / Biso mean: 30.1142 Å2 / Biso min: 10.3 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→38.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Rfactor Rfree error: 0
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