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Yorodumi- PDB-1iv3: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iv3 | ||||||
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Title | Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form MG atoms) | ||||||
Components | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | LYASE / isoprenoid / non-mevalonate / synthase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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 / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Kishida, H. / Wada, T. / Unzai, S. / Kuzuyama, T. / Terada, T. / Sirouzu, M. / Yokoyama, S. / Tame, J.R.H. / Park, S.-Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis. Authors: Kishida, H. / Wada, T. / Unzai, S. / Kuzuyama, T. / Takagi, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / Tame, J.R. / Park, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iv3.cif.gz | 195.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iv3.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 1iv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iv3_validation.pdf.gz | 405.5 KB | Display | wwPDB validaton report |
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Full document | 1iv3_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 1iv3_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1iv3_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1iv3 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1iv3 | HTTPS FTP |
-Related structure data
Related structure data | 1iv1C 1iv2C 1iv4C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16598.191 Da / Num. of mol.: 6 / Mutation: L41M, L81M, L120M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11B / Production host: Escherichia coli (E. coli) References: UniProt: Q8RQP5, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase #2: Chemical | ChemComp-MG / #3: 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: 2.1 Å3/Da / Density % sol: 41.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 / Details: PEG, pH 6.5, EVAPORATION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 5.5 / Method: vapor diffusion, hanging drop / Details: used seeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2001 / Details: mirrors |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→20 Å / Num. all: 892176 / Num. obs: 128529 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.52→1.57 Å / Rmerge(I) obs: 0.252 / % possible all: 94.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 892176 |
Reflection shell | *PLUS % possible obs: 94.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→20 Å / Num. parameters: 29959 / Num. restraintsaints: 28268 / Isotropic thermal model: Isotropic / Cross valid method: free R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7489 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 128529 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.203 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |