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Open data
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Basic information
Entry | Database: PDB / ID: 7mxz | ||||||
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Title | Sy-CrtE apo structure | ||||||
![]() | Geranylgeranyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE / Prenyl transferase / Isopentenyl pyrophosphate / Dimethylallyl pyrophosphate / cyanobacteria / terpenoids | ||||||
Function / homology | ![]() prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. / Newman, J. | ||||||
![]() | ![]() Title: Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase. Authors: Satta, A. / Esquirol, L. / Ebert, B.E. / Newman, J. / Peat, T.S. / Plan, M. / Schenk, G. / Vickers, C.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 432.3 KB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7my0C ![]() 7my1C ![]() 7my6C ![]() 7my7C ![]() 3kroS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 7 - 304 / Label seq-ID: 7 - 304
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
#1: Protein | Mass: 33476.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: PCC 6803 / Kazusa / Gene: crtE / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Droplets were 200 nL protein at 10 mg/mL plus 200 nL reservoir, 0.2 M MgCl2 and 20 %(w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→43.84 Å / Num. obs: 98723 / % possible obs: 98.2 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.47→1.49 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.805 / Num. unique obs: 4443 / CC1/2: 0.885 / Rpim(I) all: 0.334 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3kro Resolution: 1.47→39.763 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.22 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.065 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.078 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→39.763 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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