+Open data
-Basic information
Entry | Database: PDB / ID: 5d8g | ||||||
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Title | A structural view on the dissociation of E. coli Tryptophanase | ||||||
Components | Tryptophanase | ||||||
Keywords | LYASE / tryptophanase / PLP-dependent enzyme / cold dissociation / hydrophobic interactions / open conformation / closed conformation | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Almog, O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: A structural view of the dissociation of Escherichia coli tryptophanase. Authors: Green, K. / Qasim, N. / Gdaelvsky, G. / Kogan, A. / Goldgur, Y. / Parola, A.H. / Lotan, O. / Almog, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d8g.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8g.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 5d8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d8g_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 5d8g_full_validation.pdf.gz | 462.8 KB | Display | |
Data in XML | 5d8g_validation.xml.gz | 25 KB | Display | |
Data in CIF | 5d8g_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8g ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8g | HTTPS FTP |
-Related structure data
Related structure data | |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52496.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HLPEPFRIR VIEPVKRTTR AYREEAIIKS GMNPFLLDS EDVFIDLLTD SGTGAMTQS MQAAMMRGDEAYSGSRSYYALA ESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTGVR ...Details: HLPEPFRIR VIEPVKRTTR AYREEAIIKS GMNPFLLDS EDVFIDLLTD SGTGAMTQS MQAAMMRGDEAYSGSRSYYALA ESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTGVR YDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQREAE YKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDVYTECRTLCVVQEGFPTYGGLEGGAMERLAVGLYD GMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSFLLGRD PKTGKQLPCPAELLRLTIPRATYTQTHMDFIIEAFKHVKENAANIKGLTFTYEPKVLRHFTAKLKEV Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: tnaA, ind, b3708, JW3686 Production host: Escherichia coli str. 'clone D i2' (bacteria) References: UniProt: P0A853, tryptophanase |
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-Non-polymers , 6 types, 429 molecules
#2: Chemical | ChemComp-CL / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 30%(w/v) PEG 400, 100 mM HEPES pH 7.5, 200 mM MgCl2, 5 mM 2-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→49.2 Å / Num. obs: 45940 / % possible obs: 99 % / Redundancy: 6.6 % / Net I/σ(I): 10.2 |
Reflection shell | Highest resolution: 1.89 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→49.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.511 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.383 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→49.2 Å
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