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Yorodumi- PDB-6jy1: Crystal Structure of a Group II pyridoxal dependent decarboxylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jy1 | ||||||
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Title | Crystal Structure of a Group II pyridoxal dependent decarboxylase, LLP-bound form from Methanocaldococcus jannaschii at 1.72 A | ||||||
Components | L-tyrosine/L-aspartate decarboxylase | ||||||
Keywords | LYASE / PLP dependent decarboxylase / Catalytic Domain / Models / Molecular / Protein Conformation / LLP / Tyrosine / Tyrosine Decarboxylase / Structure-Activity Relationship | ||||||
Function / homology | Function and homology information methanofuran biosynthetic process / tyrosine decarboxylase / tyrosine decarboxylase activity / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / carboxylic acid metabolic process / coenzyme A biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jy1.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jy1.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jy1_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 6jy1_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 6jy1_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6jy1_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/6jy1 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/6jy1 | HTTPS FTP |
-Related structure data
Related structure data | 6ldrC 6ldsC 6ldtC 3f9tS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 47658.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Strain: DSM 2661 / Gene: mfnA, MJ0050 / Plasmid: pSpeedET Details (production host): Bacterial expression vector, arabinose or T7 induced expression, kanamycin resistance Production host: Escherichia coli B (bacteria) / Strain (production host): B References: UniProt: Q60358, aspartate 1-decarboxylase, tyrosine decarboxylase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.54 % |
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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: 1.72→51.96 Å / Num. obs: 64532 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 23.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.024 / Rrim(I) all: 0.071 / Net I/σ(I): 1.72 / Num. measured all: 531270 / Scaling rejects: 1512 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F9T Resolution: 1.72→45.716 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.74 Å2 / Biso mean: 32.5925 Å2 / Biso min: 11.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.72→45.716 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: 23
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