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Yorodumi- PDB-5hxo: Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase with D71M,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hxo | ||||||
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Title | Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase with D71M, E75A and H103Y Mutants | ||||||
Components | (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic | ||||||
Keywords | TRANSFERASE / prenyltransferase | ||||||
Function / homology | Function and homology information (2Z,6Z)-farnesyl diphosphate synthase / 2-cis,6-cis-farnesyl pyrophosphate synthase activity / prenyltransferase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Solanum habrochaites (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Lee, C.C. / Chan, Y.T. / Wang, A.H.J. | ||||||
Citation | Journal: Acs Omega / Year: 2017 Title: Crystal Structure and Potential Head-to-Middle Condensation Function of aZ,Z-Farnesyl Diphosphate Synthase. Authors: Chan, Y.T. / Ko, T.P. / Yao, S.H. / Chen, Y.W. / Lee, C.C. / Wang, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hxo.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hxo.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/5hxo ftp://data.pdbj.org/pub/pdb/validation_reports/hx/5hxo | HTTPS FTP |
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-Related structure data
Related structure data | 5hxnC 5hxpC 1jp3S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | ( Mass: 26783.754 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-303 / Mutation: E75A, H103Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum habrochaites (plant) / Gene: ZFPS / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: B8XA40, (2Z,6Z)-farnesyl diphosphate synthase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 5% (w/v) PEG 8000, 40% MPD, 0.1 M Cacodylate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→25 Å / Num. obs: 15682 / % possible obs: 99.9 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 42.8 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.412 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JP3 Resolution: 2.05→24.78 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.261 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.175 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.691 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→24.78 Å
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Refine LS restraints |
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