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Yorodumi- PDB-7d9l: Crystal structure of E. coli Grx2: Enzyme inhibited state in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d9l | |||||||||
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Title | Crystal structure of E. coli Grx2: Enzyme inhibited state in complex with Zinc and glutathione sulfinic acid | |||||||||
Components | Glutaredoxin | |||||||||
Keywords | OXIDOREDUCTASE / E. coli / GRX2 / Zinc / Glutathione sulfinic acid / Enzyme inhibition | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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: Enzyme inhibited state in complex with Zinc and glutathione sulfinic acid Authors: Sreekumar, S.N. / Arockiasamy, A. #1: Journal: J Mol Biol / Year: 2001 Title: Solution structure of Escherichia coli glutaredoxin-2 shows similarity to mammalian glutathione-S-transferases. Authors: Xia, B. / Vlamis-Gardikas, A. / Holmgren, A. / Wright, P.E. / Dyson, H.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d9l.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d9l.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 7d9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d9l_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7d9l_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7d9l_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7d9l_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/7d9l ftp://data.pdbj.org/pub/pdb/validation_reports/d9/7d9l | 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24383.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: grxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TEC2 |
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-Non-polymers , 6 types, 162 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-GSF / | #6: Chemical | ChemComp-OXY / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.11 Å3/Da / Density % sol: 41.81 % / Description: 2D plates. |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA 0.01M Zinc sulfate heptahydrate, 0.1M MES monohydrate pH6.5, 25%v/v Polyethylene glycol monomethyl ether 550, Protein and ...Details: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA 0.01M Zinc sulfate heptahydrate, 0.1M MES monohydrate pH6.5, 25%v/v Polyethylene glycol monomethyl ether 550, Protein and reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with drop size 150 nl. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.35 Å / Num. obs: 28045 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.082 / Rrim(I) all: 0.208 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.6→1.628 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.207 / Num. unique obs: 1401 / CC1/2: 0.555 / Rpim(I) all: 0.525 / Rrim(I) all: 1.32 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KX4 Resolution: 1.61→42.319 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.591 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.08 / 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: 64.55 Å2 / Biso mean: 13.839 Å2 / Biso min: 5.17 Å2
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Refinement step | Cycle: final / Resolution: 1.61→42.319 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.648 Å / Rfactor Rfree error: 0
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