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- PDB-8cdf: Structure of glutarate hydroxylase (GlaH) from Escherichia coli a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cdf | ||||||
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Title | Structure of glutarate hydroxylase (GlaH) from Escherichia coli at a resolution of 1.8 angstrom obtained as a contaminant during routine use of E. coli as an expression host | ||||||
![]() | Glutarate 2-hydroxylase | ||||||
![]() | METAL BINDING PROTEIN / Carbon-starvation induced / hydroxylase / non haem Fe (II)-dependent oxygenase | ||||||
Function / homology | ![]() glutarate dioxygenase activity / glutarate dioxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated / L-lysine catabolic process / ferrous iron binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Adeyeye, A.A. / Schubert, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of glutarate hydroxylase (GlaH) from Escherichia coli at a resolution of 1.8 angstrom obtained as a contaminant during routine use of E. coli as an expression host Authors: Adeyeye, A.A. / Schubert, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.8 KB | Display | ![]() |
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PDB format | ![]() | 57.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 924.8 KB | Display | ![]() |
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Full document | ![]() | 926 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
#1: Protein | Mass: 35974.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: csiD, glaH, ACU57_06710, AM464_04980, BGM66_004646, BJI68_04905, C5N07_05545, CTR35_002510, EIZ93_05365, EL79_1036, FOI11_00325, FOI11_022855, FV293_23215, FWK02_21895, G3V95_09995, GIB53_ ...Gene: csiD, glaH, ACU57_06710, AM464_04980, BGM66_004646, BJI68_04905, C5N07_05545, CTR35_002510, EIZ93_05365, EL79_1036, FOI11_00325, FOI11_022855, FV293_23215, FWK02_21895, G3V95_09995, GIB53_09245, GJO56_18475, GKF89_16305, GNW61_23135, GRW05_29650, GRW24_16590, GRW56_10550, GRW57_12335, HMV95_03335, J0541_002578, JNP96_20920, NCTC9045_01367, NCTC9073_04720, NCTC9117_01751, SAMEA3751407_03408 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FE2 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.64 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 47 mM K3PO4, 0.4 M (NH4)2SO4, 200 mM KCl, 1mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→53.37 Å / Num. obs: 49508 / % possible obs: 99.95 % / Redundancy: 11.9 % / Biso Wilson estimate: 33.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.106 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2412 / CC1/2: 0.4 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→50.35 Å
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Refine LS restraints |
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LS refinement shell |
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