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Open data
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Basic information
Entry | Database: PDB / ID: 8gzi | ||||||
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Title | Crystal Structure of ApiI in complex with SAH | ||||||
![]() | ApiI | ||||||
![]() | BIOSYNTHETIC PROTEIN / complex | ||||||
Function / homology | S-ADENOSYL-L-HOMOCYSTEINE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, J.H. / Lu, J.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of ApiI in complex with SAH Authors: Zhou, J.H. / Lu, J.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.6 KB | Display | ![]() |
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PDB format | ![]() | 66.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 734.5 KB | Display | ![]() |
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Full document | ![]() | 741.2 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wupS S: Starting model for refinement |
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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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43680.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium chloride, 0.1 M MES pH6, 20%(w/v)PEG 2000 MME |
-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: Nov 8, 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: 2.12→37.522 Å / Num. obs: 25591 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 32.7129451443 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.028 / Rsym value: 0.092 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1855 / CC1/2: 0.996 / Rpim(I) all: 0.185 / Rrim(I) all: 0.606 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WUP Resolution: 2.12209677016→37.5214098838 Å / SU ML: 0.243882300324 / Cross valid method: FREE R-VALUE / σ(F): 1.33646519919 / Phase error: 25.2735300356 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: 45.2051386468 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12209677016→37.5214098838 Å
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Refine LS restraints |
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LS refinement shell |
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