+Open data
-Basic information
Entry | Database: PDB / ID: 2vnp | |||||||||
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Title | Monoclinic form of IDI-1 | |||||||||
Components | ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE | |||||||||
Keywords | ISOMERASE / ISOPRENE BIOSYNTHESIS / POLYMORPHISM / METAL-BINDING / IPP ISOMERASE / MANGANESE / CYTOPLASM / MAGNESIUM | |||||||||
Function / homology | Function and homology information isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / dimethylallyl diphosphate biosynthetic process / isoprenoid biosynthetic process / DNA damage response / magnesium ion binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | |||||||||
Authors | de Ruyck, J. / Oudjama, Y. / Wouters, J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Monoclinic Form of Isopentenyl Diphosphate Isomerase: A Case of Polymorphism in Biomolecular Crystals. Authors: De Ruyck, J. / Oudjama, Y. / Wouters, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vnp.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vnp.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vnp_validation.pdf.gz | 458.1 KB | Display | wwPDB validaton report |
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Full document | 2vnp_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 2vnp_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 2vnp_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/2vnp ftp://data.pdbj.org/pub/pdb/validation_reports/vn/2vnp | HTTPS FTP |
-Related structure data
Related structure data | 2vnqC 1hx3S 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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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: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 4 - 179 / Label seq-ID: 4 - 179
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-Components
#1: Protein | Mass: 20644.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q46822, isopentenyl-diphosphate Delta-isomerase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.25 Å3/Da / Density % sol: 44.81 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 18119 / % possible obs: 97.8 % / Observed criterion σ(I): 4 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.2→2.4 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HX3 Resolution: 2.19→36.2 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.111 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.234 / 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: 23.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→36.2 Å
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Refine LS restraints |
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