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Yorodumi- PDB-2xwl: Crystal structure of IspD from Mycobacterium smegmatis in complex... -
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-Basic information
Entry | Database: PDB / ID: 2xwl | ||||||
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Title | Crystal structure of IspD from Mycobacterium smegmatis in complex with CTP and Mg | ||||||
Components | 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / MEP PATHWAY | ||||||
Function / homology | Function and homology information 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Bjorkelid, C. / Bergfors, T. / Unge, T. / Jones, T.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Structural and Functional Studies on Mycobacterial Ispd Enzymes Authors: Bjorkelid, C. / Bergfors, T. / Henriksson, L.M. / Stern, A.L. / Unge, T. / Mowbray, S.L. / Jones, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xwl.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xwl.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xwl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2xwl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xwl_validation.xml.gz | 23 KB | Display | |
Data in CIF | 2xwl_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/2xwl ftp://data.pdbj.org/pub/pdb/validation_reports/xw/2xwl | HTTPS FTP |
-Related structure data
Related structure data | 2xwmC 2xwnC 1vgtS C: citing same article (ref.) 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: (Code: given Matrix: (-0.7586, 0.6223, 0.1932), Vector: |
-Components
#1: Protein | Mass: 22667.855 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 / Plasmid: PEXP5CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI References: UniProt: A0R560, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase #2: Chemical | #3: Chemical | #4: 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: 2.17 Å3/Da / Density % sol: 43.23 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. DROPS WITH 300 NANOLITERS PROTEIN SOLUTION (PROTEIN AT 40 MG/ML IN 20 MM BIS-TRIS-PROPANE, PH 6.5, 0.1 M NACL WITH 10 MM CTP AND 10 MM MGCL2) ...Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. DROPS WITH 300 NANOLITERS PROTEIN SOLUTION (PROTEIN AT 40 MG/ML IN 20 MM BIS-TRIS-PROPANE, PH 6.5, 0.1 M NACL WITH 10 MM CTP AND 10 MM MGCL2) AND 300 NANOLITERS SCREENING/RESERVOIR SOLUTION (10% (W/V) PEG 8000, 20% (V/V) ETHYLENE GLYCOL, 0.03 M EACH OF DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, TETRAETHYLENEGLYCOL, PENTAETHYLENEGLYCOL AND 0.1 M MES/IMIDAZOLE BUFFERS PH 6.5) |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0045 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0045 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→38.5 Å / Num. obs: 64486 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.49→1.57 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.3 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VGT Resolution: 1.49→61.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.203 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
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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: 23.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→61.95 Å
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Refine LS restraints |
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