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Yorodumi- PDB-7dkp: Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dkp | |||||||||
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Title | Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution | |||||||||
Components | Glutaredoxin | |||||||||
Keywords | OXIDOREDUCTASE / E. coli Grx2 / GSH | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Sreekumar, S.N. / Arockiasamy, A. | |||||||||
Funding support | India, 2items
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Citation | Journal: To Be Published Title: Crystal structure of E. coli Grx2 in complex with GSH at 1.45 A resolution Authors: Sreekumar, S.N. / Arockiasamy, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dkp.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dkp.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 7dkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dkp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7dkp_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7dkp_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 7dkp_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/7dkp ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dkp | HTTPS FTP |
-Related structure data
Related structure data | 4kx4S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 24383.229 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TEC2 #2: Chemical | ChemComp-GSH / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: 2D plates |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA Reservoir condition: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v ...Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA Reservoir condition: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000. Protein and reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with drop size of 150 nl. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.449→42.94 Å / Num. obs: 137631 / % possible obs: 94.7 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.055 / Rrim(I) all: 0.113 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.449→1.476 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.635 / Num. unique obs: 6882 / CC1/2: 0.759 / Rpim(I) all: 0.349 / Rrim(I) all: 0.726 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KX4 Resolution: 1.45→42.893 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.027 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 48.92 Å2 / Biso mean: 11.935 Å2 / Biso min: 6.22 Å2
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Refinement step | Cycle: final / Resolution: 1.45→42.893 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Rfactor Rfree error: 0
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