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Yorodumi- PDB-2zrv: Crystal structure of Sulfolobus shibatae isopentenyl diphosphate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zrv | ||||||
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Title | Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN. | ||||||
Components | Isopentenyl-diphosphate delta-isomeraseIsopentenyl-diphosphate delta isomerase | ||||||
Keywords | ISOMERASE / type 2 / IDI / FMN / isopentenyl diphosphate isomerase / reduced form / Flavoprotein / Isoprene biosynthesis / NADP | ||||||
Function / homology | Function and homology information isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / isoprenoid biosynthetic process / NADPH binding / FMN binding / oxidoreductase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus shibatae (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Unno, H. / Yamashita, S. / Ikeda, Y. / Sekiguchi, S. / Yoshida, N. / Yoshimura, T. / Kusunoki, M. / Nakayama, T. / Nishino, T. / Hemmi, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase. Authors: Unno, H. / Yamashita, S. / Ikeda, Y. / Sekiguchi, S.Y. / Yoshida, N. / Yoshimura, T. / Kusunoki, M. / Nakayama, T. / Nishino, T. / Hemmi, H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zrv.cif.gz | 293.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zrv.ent.gz | 239.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/2zrv ftp://data.pdbj.org/pub/pdb/validation_reports/zr/2zrv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 40475.816 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: fni, idi / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) References: UniProt: P61615, isopentenyl-diphosphate Delta-isomerase #2: Chemical | ChemComp-FNR / #3: 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: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 30% PEG 400, 0.2M sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0000, 1.13980, 1.14022, 1.04000 | |||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2008 / Details: mirror | |||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 77757 / % possible obs: 98.7 % / Redundancy: 9 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 22.7 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→49.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.36 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.203 / 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: 31.858 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→49.03 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.301→2.36 Å / Total num. of bins used: 20
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