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Yorodumi- PDB-4w1y: Crystal structure of Escherichia coli Tryptophanase in 'semi-holo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w1y | |||||||||
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Title | Crystal structure of Escherichia coli Tryptophanase in 'semi-holo' form | |||||||||
Components | (Tryptophanase) x 2 | |||||||||
Keywords | LYASE / Tryptophanase | |||||||||
Function / homology | Function and homology information indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / tryptophan catabolic process / potassium ion binding / pyridoxal phosphate binding / protein-containing complex / identical protein binding ...indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / tryptophan catabolic process / potassium ion binding / pyridoxal phosphate binding / protein-containing complex / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3.2 Å | |||||||||
Authors | Goldgur, Y. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Structures of Escherichia coli tryptophanase in holo and `semi-holo' forms. Authors: Kogan, A. / Raznov, L. / Gdalevsky, G.Y. / Cohen-Luria, R. / Almog, O. / Parola, A.H. / Goldgur, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w1y.cif.gz | 187.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w1y.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 4w1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w1y_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
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Full document | 4w1y_full_validation.pdf.gz | 555.2 KB | Display | |
Data in XML | 4w1y_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 4w1y_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/4w1y ftp://data.pdbj.org/pub/pdb/validation_reports/w1/4w1y | HTTPS FTP |
-Related 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: 52540.801 Da / Num. of mol.: 1 / Fragment: UNP residues 5-471 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tnaA, ind, b3708, JW3686 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A853, tryptophanase | ||
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#2: Protein | Mass: 52312.684 Da / Num. of mol.: 1 / Fragment: UNP residues 5-471 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tnaA, ind, b3708, JW3686 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A853, tryptophanase | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 13-16 % AMMONIUM SULFATE, 1-5 MM PLP, 50 MM TRIS / PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→15 Å / Num. obs: 22389 / % possible obs: 94.8 % / Redundancy: 5.9 % / Rsym value: 0.124 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.1 / % possible all: 97.2 |
-Processing
Software | Name: REFMAC / Version: 5.4.0077 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.887 / SU B: 24.855 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.274 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→15 Å
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