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Yorodumi- PDB-6th5: Crystal structure of mature wildtype primitive Phytochelatin synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6th5 | ||||||
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Title | Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975 | ||||||
Components | Alr0975 protein | ||||||
Keywords | TRANSFERASE / Phytochelatin / heavy-metal detoxification / glutathione / gamma-glutamyl cysteine | ||||||
Function / homology | Function and homology information glutathione gamma-glutamylcysteinyltransferase / glutathione gamma-glutamylcysteinyltransferase activity / phytochelatin biosynthetic process / response to metal ion / metal ion binding Similarity search - Function | ||||||
Biological species | Nostoc sp. PCC 7120 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Feiler, C.G. / Blankenfeldt, W. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975 Authors: Feiler, C.G. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6th5.cif.gz | 216.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6th5.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 6th5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6th5_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 6th5_full_validation.pdf.gz | 439.9 KB | Display | |
Data in XML | 6th5_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 6th5_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6th5 ftp://data.pdbj.org/pub/pdb/validation_reports/th/6th5 | HTTPS FTP |
-Related structure data
Related structure data | 2btwS 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: 24643.889 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: alr0975, alr0975 / Plasmid: p10$ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YY76 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 16% PEG 8000, 0.1 M MES pH 5.5, 0.2 M calcium acetate PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 15, 2012 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→34.26 Å / Num. obs: 26211 / % possible obs: 97.38 % / Redundancy: 2.2 % / Biso Wilson estimate: 20.61 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.0975 / Rrim(I) all: 0.151 / Net I/σ(I): 6.59 |
Reflection shell | Resolution: 1.99→2.061 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 4465 / CC1/2: 0.845 / Rpim(I) all: 0.57 / Rrim(I) all: 0.879 / % possible all: 98.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BTW Resolution: 1.99→34.26 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1224
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→34.26 Å
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Refine LS restraints |
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LS refinement shell |
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