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Yorodumi- PDB-3n9w: Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidyly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n9w | ||||||
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Title | Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) in complex with 1,2-Propanediol | ||||||
Components | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / YGBP / CYTIDYLYLTRANSFERASE / DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXP) / ISOPRENOID BIOSYNTHESIS / 1 / 2-Propanediol / FBLD | ||||||
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 / magnesium ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Behnen, J. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2012 Title: Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Authors: Behnen, J. / Koster, H. / Neudert, G. / Craan, T. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n9w.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n9w.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 3n9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n9w_validation.pdf.gz | 462 KB | Display | wwPDB validaton report |
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Full document | 3n9w_full_validation.pdf.gz | 470 KB | Display | |
Data in XML | 3n9w_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 3n9w_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/3n9w ftp://data.pdbj.org/pub/pdb/validation_reports/n9/3n9w | HTTPS FTP |
-Related structure data
Related structure data | 3ms3C 3msaC 3msfC 3msnC 3n21C 3n4aC 3nn7C 3nx8C 3pczC 3prsC 3pvkC 3pwwC 1vgtS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 25641.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 References: UniProt: Q46893, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase #2: Chemical | #3: Chemical | ChemComp-PGR / | #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: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% 1,2-propanediol, 20% PEG400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2009 |
Radiation | Monochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 32991 / Num. obs: 32991 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.049 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.287 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VGT Resolution: 1.9→10 Å / Num. parameters: 12823 / Num. restraintsaints: 16547 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 3086 / Occupancy sum non hydrogen: 3177 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.93 Å / Num. reflection Rfree: 3287 |