+Open data
-Basic information
Entry | Database: PDB / ID: 8h92 | ||||||
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Title | Ziziphus jujuba adenylyl cyclase | ||||||
Components | triphosphate tunel metalloenzyme 3-like | ||||||
Keywords | PLANT PROTEIN / CYTH_like domain / Cyclase | ||||||
Function / homology | CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / pyrophosphatase activity / Triphosphate tunel metalloenzyme 3-like Function and homology information | ||||||
Biological species | Ziziphus jujuba (common jujube) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Liu, Z.G. / Wang, L.L. / Yuan, Y. / Liu, M.J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: A super plant adenylyl cyclase-ZjAC Authors: Liu, Z.G. / Yuan, Y. / Wang, L.L. / Zhao, X. / Wang, L.X. / Wang, L.H. / Zhao, Z.H. / Zhao, J. / Dai, L. / Wang, J.R. / Liu, P. / Liu, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h92.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h92.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 8h92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/8h92 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/8h92 | HTTPS FTP |
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-Related structure data
Related structure data | 5a5yS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 6 - 204 / Label seq-ID: 6 - 204
NCS oper: (Code: givenMatrix: (-0.99971103939, -0.0112285595323, 0.0212545800585), (-0.0185226508927, -0.203742304183, -0.978849316744), (0.0153215249418, -0.978960159014, 0.203475447994)Vector: 42. ...NCS oper: (Code: given Matrix: (-0.99971103939, -0.0112285595323, 0.0212545800585), Vector: |
-Components
#1: Protein | Mass: 23741.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ziziphus jujuba (common jujube) / Gene: LOC107415651 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A6P3ZKP6 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.83 Å3/Da / Density % sol: 56.56 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2021 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 17244 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.059 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 9.2 / Num. unique obs: 850 / Rpim(I) all: 0.367 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A5Y Resolution: 2.6→28.57 Å / SU ML: 0.3097 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4677 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→28.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.941172609643 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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