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Yorodumi- PDB-2uzh: Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uzh | ||||||
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Title | Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) | ||||||
Components | 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE | ||||||
Keywords | LYASE / ISPF / MYCOBACTERIA / COMPLEX WITH CDP / NON-MEVALONATE PATHWAY OF ISOPRENOID 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 / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Buetow, L. / Brown, A.C. / Parish, T. / Hunter, W.N. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2007 Title: The Structure of Mycobacteria 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase, an Essential Enzyme, Provides a Platform for Drug Discovery. Authors: Buetow, L. / Brown, A.C. / Parish, T. / 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 | 2uzh.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzh.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 2uzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uzh_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 2uzh_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 2uzh_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 2uzh_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzh ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzh | HTTPS FTP |
-Related structure data
Related structure data | 1gx1S S: Starting model for refinement |
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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:
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 16758.922 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: EACH CONTAINS A ZN CATION, WHICH IS REQUIRED FOR ACTIVITY, AND CDP, A FRAGMENT OF SUBSTRATE. Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC(2)155 / Plasmid: PET15TEV (VARIANT OF PET15B FROM NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0R559, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 8 types, 287 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-IPE / | #7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | FIRST TWO AMINO ACIDS OF SEQUENCE CORRESPOND |
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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: 3.15 Å3/Da / Density % sol: 60.64 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 18% PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M CALCIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 20, 2006 Details: PT COATED MIRRORS IN A KIRKPATRICK-BAEZ (KB) GEOMETRY |
Radiation | Monochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→51.3 Å / Num. obs: 33193 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.7 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GX1 Resolution: 2.2→51.3 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.085 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→51.3 Å
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Refine LS restraints |
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