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- PDB-2bu3: Acyl-enzyme intermediate between Alr0975 and glutathione at pH 3.4 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bu3 | ||||||
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Title | Acyl-enzyme intermediate between Alr0975 and glutathione at pH 3.4 | ||||||
![]() | ALR0975 PROTEIN | ||||||
![]() | TRANSFERASE / PHYTOCHELATIN SYNTHASE / PCS / ALR0975 / ACYL-ENZYME INTERMEDIATE / NOSTOC / GLUTATHIONE METABOLISM / CYSTEINE PROTEASE | ||||||
Function / homology | ![]() glutathione gamma-glutamylcysteinyltransferase / glutathione gamma-glutamylcysteinyltransferase activity / phytochelatin biosynthetic process / response to metal ion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vivares, D. / Arnoux, P. / Pignol, D. | ||||||
![]() | ![]() Title: A Papain-Like Enzyme at Work: Native and Acyl- Enzyme Intermediate Structures in Phytochelatin Synthesis. Authors: Vivares, D. / Arnoux, P. / Pignol, D. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Characterization of Phytochelatin Synthase-Like Protein Encoded by Alr0975 from a Prokaryote, Nostoc Sp. Pcc 7120 Authors: Tsuji, N. / Nishikori, S. / Iwabe, O. / Shiraki, K. / Miyasaka, H. / Takagi, M. / Hirata, K. / Miyamoto, K. #2: Journal: Phytochemistry / Year: 2004 Title: A Cyanobacterial Protein with Similarity to Phytochelatin Synthases Catalyzes the Conversion of Glutathione to Gamma-Glutamylcysteine and Lacks Phytochelatin Synthase Activity Authors: Harada, E. / Von Roepenack-Lahaye, E. / Clemens, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.1 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 918.8 KB | Display | ![]() |
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Full document | ![]() | 924.4 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2btwSC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.51157, 0.53057, 0.67586), Vector: |
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Components
#1: Protein | Mass: 29437.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8YY76, glutathione gamma-glutamylcysteinyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE PUTATIVE N-TERMINAL SECRETION SIGNAL WAS NOT INCLUDED IN THE PLASMID CONSTRUCTI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | pH: 3.2 / Details: pH 3.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→29 Å / Num. obs: 87418 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BTW Resolution: 1.4→29.59 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.477 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARGININE 180 IS DISORDERED AND WAS MODELED AS A GLYCINE
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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: 10.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→29.59 Å
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Refine LS restraints |
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