+Open data
-Basic information
Entry | Database: PDB / ID: 8gx4 | ||||||
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Title | Crystal structure of Diels-Alderase ApiI in complex with SAM | ||||||
Components | ApiI | ||||||
Keywords | BIOSYNTHETIC PROTEIN | ||||||
Function / homology | TRIETHYLENE GLYCOL / S-ADENOSYLMETHIONINE Function and homology information | ||||||
Biological species | Apiospora montagnei NRRL 25634 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97007775894 Å | ||||||
Authors | Zhou, J.H. / Lu, J.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Diels-Alderase ApiI in complex with SAM Authors: Zhou, J.H. / Lu, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gx4.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gx4.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gx4_validation.pdf.gz | 756.4 KB | Display | wwPDB validaton report |
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Full document | 8gx4_full_validation.pdf.gz | 765.3 KB | Display | |
Data in XML | 8gx4_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 8gx4_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/8gx4 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/8gx4 | HTTPS FTP |
-Related structure data
Related structure data | 7wupS 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43680.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apiospora montagnei NRRL 25634 (fungus) Production host: Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 168 molecules
#2: Chemical | ChemComp-SAM / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.59 Å3/Da / Density % sol: 52.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES/NaOH PH=7.0, 0.2 M NaCl, 20%(w/v)PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→23.51 Å / Num. obs: 32051 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 36.067981888 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.97→2.02 Å / Rmerge(I) obs: 1.267 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 318124 / CC1/2: 0.882 / Rpim(I) all: 0.462 / Rrim(I) all: 1.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WUP Resolution: 1.97007775894→21.291234552 Å / SU ML: 0.220133981946 / Cross valid method: FREE R-VALUE / σ(F): 1.34219864499 / Phase error: 25.252094625 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: 47.8281266322 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97007775894→21.291234552 Å
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Refine LS restraints |
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LS refinement shell |
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