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- PDB-1gx1: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gx1 | ||||||
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Title | Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase | ||||||
![]() | 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE | ||||||
![]() | SYNTHASE / ISOPRENOID / LYASE / ISOPRENE BIOSYNTHESIS | ||||||
Function / homology | ![]() 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / ubiquinone biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / manganese ion binding / zinc ion binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kemp, L.E. / Bond, C.S. / Hunter, W.N. | ||||||
![]() | ![]() Title: Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase: An Essential Enzyme for Isoprenoid Biosynthesis and Target for Antimicrobial Drug Development Authors: Kemp, L.E. / Bond, C.S. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.483668, 0.118894, -0.867139), Vector: |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 17237.229 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P36663, UniProt: P62617*PLUS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 5 types, 309 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CDP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CDP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.3 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 10-20% PEG 2000 MONOETHYL ETHER, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, pH 4.60 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2001 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→30 Å / Num. obs: 91076 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 1.7 / % possible all: 73.8 | ||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 50289 / % possible obs: 97.4 % / Num. measured all: 193317 / Rmerge(I) obs: 0.067 | ||||||||||||
Reflection shell | *PLUS % possible obs: 89.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THERE ARE RESIDUES WHOSE SIDECHAINS COULD NOT BE FITTED. THESE ARE INCLUDED IN THE PDB FILE WITH ZERO OCCUPANCY
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor obs: 0.18 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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