+Open data
-Basic information
Entry | Database: PDB / ID: 7my1 | ||||||
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Title | Sy-CrtE structure with IPP, N-term His-tag | ||||||
Components | Geranylgeranyl pyrophosphate synthase | ||||||
Keywords | TRANSFERASE / Prenyl transferase / Isopentenyl pyrophosphate / Dimethylallyl pyrophosphate / cyanobacteria / terpenoids | ||||||
Function / homology | Function and homology information prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Peat, T.S. / Newman, J. | ||||||
Citation | Journal: Febs J. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7my1.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7my1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7my1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/7my1 ftp://data.pdbj.org/pub/pdb/validation_reports/my/7my1 | HTTPS FTP |
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-Related structure data
Related structure data | 7mxzSC 7my0C 7my6C 7my7C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 34707.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / Gene: crtE / Production host: Escherichia coli (E. coli) / References: UniProt: P72683 | ||||||
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#2: Chemical | ChemComp-IPE / | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein was at 10 mg/mL and the drops were 200 nL plus 200 nL with the reservoir being 22.5% PEG 3350, 0.3M MgCl2, 0.1M Na-HEPES pH 6.55 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 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: 1.84→45.16 Å / Num. obs: 24629 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.84→1.88 Å / Rmerge(I) obs: 1.367 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1295 / CC1/2: 0.574 / Rpim(I) all: 0.587 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7mxz Resolution: 1.84→45.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.61 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.135 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: 30.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→45.16 Å
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Refine LS restraints |
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LS refinement shell |
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