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Open data
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Basic information
Entry | Database: PDB / ID: 8ckh | ||||||
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Title | Crystal structure of IspE from Klebsiella pneumoniae | ||||||
![]() | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | ||||||
![]() | PROTEIN BINDING / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE / IspE / Klebsiella pneumoniae. | ||||||
Function / homology | ![]() 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase / 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hamid, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of IspE from Klebsiella pneumoniae Authors: Hamid, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.1 KB | Display | ![]() |
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PDB format | ![]() | 186.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 37 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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Unit cell |
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Components
#1: Protein | Mass: 30856.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ispE, ipk, B5L96_11675, BN49_3345, FXN67_13605, GNE24_13115, GNG14_12250, NCTC13465_02970, NCTC13635_07143, NCTC5052_02044, NCTC9140_05240, NCTC9601_01067, NCTC9661_03960, SAMEA3499874_01580, ...Gene: ispE, ipk, B5L96_11675, BN49_3345, FXN67_13605, GNE24_13115, GNG14_12250, NCTC13465_02970, NCTC13635_07143, NCTC5052_02044, NCTC9140_05240, NCTC9601_01067, NCTC9661_03960, SAMEA3499874_01580, SAMEA3499901_04677, SAMEA3538828_04749 Production host: ![]() ![]() References: UniProt: W9BPL2, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.16 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH7.0 1 M Sodium citrate / PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0007 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.58 Å / Num. obs: 46367 / % possible obs: 98.53 % / Redundancy: 6.3 % / Biso Wilson estimate: 26.99 Å2 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.087 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.8→1.8 Å / Num. unique obs: 4526 / Rrim(I) all: 0.695 / % possible all: 97.41 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→44.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 39.1260751016 Å / Origin y: 24.3356078802 Å / Origin z: 73.5618338654 Å
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Refinement TLS group | Selection details: all |