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Yorodumi- PDB-6lds: Structure of a K245A mutant of L-tyrosine decarboxylase from Meth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lds | ||||||
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Title | Structure of a K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii complexed with L-Tyr: External aldimine form | ||||||
Components | L-tyrosine/L-aspartate decarboxylase | ||||||
Keywords | LYASE / PLP dependent decarboxylase / Catalytic Domain / Models / Molecular / Protein Conformation / PLP / Tyrosine / External aldimine / Tyrosine Decarboxylase / Structure-Activity Relationship / Dunathan alignment | ||||||
Function / homology | Function and homology information methanofuran biosynthetic process / tyrosine decarboxylase / tyrosine decarboxylase activity / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / coenzyme A biosynthetic process / carboxylic acid metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Manoj, N. / Gayathri, S.C. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 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: Journal: J. Struct. Biol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lds.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lds.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/6lds ftp://data.pdbj.org/pub/pdb/validation_reports/ld/6lds | HTTPS FTP |
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-Related structure data
Related structure data | 6jy1C 6ldrSC 6ldtC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47600.730 Da / Num. of mol.: 1 / Mutation: K245A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: mfnA, MJ0050 / Plasmid: pSpeedET / Details (production host): Bacterial expression vector / Production host: Escherichia coli B (bacteria) / Strain (production host): B References: UniProt: Q60358, aspartate 1-decarboxylase, tyrosine decarboxylase | ||||||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-0PR / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Nonpolymer details | Authors state that the ligand in this entry has a protonated N1 atom and the corresponding hydrogen ...Authors state that the ligand in this entry has a protonated N1 atom and the corresponding hydrogen atom is labelled as H1. This is a different form of 0PR. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.37 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2015 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→51.86 Å / Num. obs: 58830 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.028 / Rrim(I) all: 0.083 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.77→1.81 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.179 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3301 / CC1/2: 0.824 / Rpim(I) all: 0.465 / Rrim(I) all: 1.272 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LDR Resolution: 1.8→49.21 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 90.35 Å2 / Biso mean: 29.914 Å2 / Biso min: 12.73 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→49.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.83 Å / Rfactor Rfree error: 0
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