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Yorodumi- PDB-1gx1: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gx1 | ||||||
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Title | Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase | ||||||
Components | 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE | ||||||
Keywords | SYNTHASE / ISOPRENOID / LYASE / ISOPRENE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 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 | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Kemp, L.E. / Bond, C.S. / Hunter, W.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gx1.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gx1.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gx1 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gx1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.483668, 0.118894, -0.867139), Vector: |
-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.) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli / Description: SYNTHETIC GENE / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) 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
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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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: 2.4 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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9184,0.9786,0.9788 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→20 Å / SU B: 2.473 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 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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