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- PDB-6ldr: Structure of a K245A mutant of a Group II PLP dependent decarboxy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ldr | ||||||
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Title | Structure of a K245A mutant of a Group II PLP dependent decarboxylase from Methanocaldococcus jannaschii, in complex with PLP | ||||||
![]() | L-tyrosine/L-aspartate decarboxylase | ||||||
![]() | LYASE / PLP dependent decarboxylase / Catalytic Domain / Protein Conformation / Pyridoxal 5-phosphate / Lys mutant / Group II 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. / Gayathri, S.C. | ||||||
![]() | ![]() 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. #1: ![]() Title: Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. Authors: Gayathri, S.C. / 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 | ![]() | 163.5 KB | Display | ![]() |
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PDB format | ![]() | 125.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jy1SC ![]() 6ldsC ![]() 6ldtC S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47600.730 Da / Num. of mol.: 1 / Mutation: K245A 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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-Non-polymers , 5 types, 331 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / | ||||
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#3: Chemical | ChemComp-NH4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M sodium citrate pH 5.4, 0.2M sodium potassium tartarate, 2.0M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2015 |
Radiation | Monochromator: S1 (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→49.19 Å / Num. obs: 56951 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 23.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.031 / Rrim(I) all: 0.097 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.119 / Num. unique obs: 3322 / CC1/2: 0.852 / Rpim(I) all: 0.382 / Rrim(I) all: 1.184 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JY1 Resolution: 1.79→45.82 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.59 Å2 / Biso mean: 28.0014 Å2 / Biso min: 10.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→45.82 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %
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