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- PDB-5hxp: Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hxp | ||||||
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Title | Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with IPP | ||||||
![]() | (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic | ||||||
![]() | TRANSFERASE / prenyltransferase | ||||||
Function / homology | ![]() (2Z,6Z)-farnesyl diphosphate synthase / 2-cis,6-cis-farnesyl pyrophosphate synthase activity / plastid membrane organization / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / chloroplast stroma / response to cold / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, C.C. / Chan, Y.T. / Wang, A.H.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 82.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hxnC ![]() 5hxoC ![]() 1jp3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26783.754 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 72-303 / Mutation: E75A, H103Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B8XA40, (2Z,6Z)-farnesyl diphosphate synthase #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 13% PEG 10K, 20mM 18-crown-6, 0.1M MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 35453 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JP3 Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.039 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.165 / 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: 23.525 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→25 Å
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Refine LS restraints |
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