+Open data
-Basic information
Entry | Database: PDB / ID: 2v2v | ||||||
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Title | IspE in complex with ligand | ||||||
Components | 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE | ||||||
Keywords | TRANSFERASE / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D- ERYTHRITOL / AQUIFEX AEOLICUS / NUCLEOTIDE-BINDING / ISOPRENE BIOSYNTHESIS / KINASE / ATP-BINDING / NON-MEVALONATE | ||||||
Function / homology | Function and homology information 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase / 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å | ||||||
Authors | Alphey, M.S. / Hunter, W.N. | ||||||
Citation | Journal: Chemmedchem / Year: 2008 Title: Synthesis and Characterization of Cytidine Derivatives that Inhibit the Kinase Ispe of the Non-Mevalonate Pathway for Isoprenoid Biosynthesis. Authors: Crane, C.M. / Hirsch, A.K. / Alphey, M.S. / Sgraja, T. / Lauw, S. / Illarionova, V. / Rohdich, F. / Eisenreich, W. / Hunter, W.N. / Bacher, A. / Diederich, F. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v2v.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2v.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2v ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2v | HTTPS FTP |
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-Related structure data
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30100.377 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O67060, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase |
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-Non-polymers , 5 types, 280 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-BR / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES -2 TO 0 ARE RESIDUAL FROM HIS-TAG REMOVAL |
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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: 3.62 Å3/Da / Density % sol: 66.01 % |
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Crystal grow | pH: 8 Details: 1.6 M (NH4)2SO4, 0.1 M NA CACODYLATE, PH 6.5, 0.1 M NABR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Oct 24, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→90 Å / Num. obs: 33908 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.4→90 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.932 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.254 / 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 / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→90 Å
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Refine LS restraints |
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