+Open data
-Basic information
Entry | Database: PDB / ID: 2vf3 | ||||||
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Title | Aquifex aeolicus IspE in complex with ligand | ||||||
Components | 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE | ||||||
Keywords | TRANSFERASE / ISPE / KINASE / AQUIFEX / ATP-BINDING / ISOPRENE BIOSYNTHESIS / NON-MEVALONATE / NUCLEOTIDE-BINDING | ||||||
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 / SYNCHROTRON / OTHER / Resolution: 2.2 Å | ||||||
Authors | Alphey, M.S. / Hunter, W.N. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2008 Title: Inhibitors of the Kinase Ispe: Structure-Activity Relationships and Co-Crystal Structure Analysis. Authors: Hirsch, A.K. / Alphey, M.S. / Lauw, S. / Seet, M. / Barandun, L. / Eisenreich, W. / Rohdich, F. / 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 | 2vf3.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vf3.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/2vf3 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/2vf3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 4 / Auth seq-ID: 0 - 2001 / Label seq-ID: 3
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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, 168 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | REMNANTS OF N-TERMINAL 6HIS-TAG PRESENT IN SEQUENCE, BUT ONLY PARTIALLY ORDERED IN STRUCTURE |
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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: 3.6 Å3/Da / Density % sol: 65.8 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 17, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→68 Å / Num. obs: 43998 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.2→97.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.093 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CL 6 HAS BEEN ADDED UNREFINED WITH AN OCCUPANCY OF 0.25 IN A POSITION PARTIALLY OCCUPIED BY LIGAND RESIDUES 22-25 NEAR THE ACTIVE SITE IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CL 6 HAS BEEN ADDED UNREFINED WITH AN OCCUPANCY OF 0.25 IN A POSITION PARTIALLY OCCUPIED BY LIGAND RESIDUES 22-25 NEAR THE ACTIVE SITE IN BOTH CHAINS APPEARS FLEXIBLE. ELECTRON DENSITY IS NOT WELL-DEFINED AND THIS IS REFLECTED IN THE GEOMETRY OF THE REGION.
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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: 46.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→97.13 Å
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Refine LS restraints |
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