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Open data
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Basic information
Entry | Database: PDB / ID: 9j7q | |||||||||
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Title | Crystal structure of S. aureus MccB with PLP | |||||||||
![]() | Cystathionine gamma-synthase homolog | |||||||||
![]() | LYASE / CGL / PLP / MccB | |||||||||
Function / homology | ![]() cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ha, N.-C. / Lee, D. / Lee, H. / Byun, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of S. aureus MccB with PLP Authors: Ha, N.-C. / Lee, D. / Lee, H. / Byun, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.2 KB | Display | ![]() |
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PDB format | ![]() | 67.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 452.7 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 41523.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: yrhB, SAV0460 / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-PEG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.73 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M Sodium Acetate trihydrate pH4.5, 30% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 50071 / % possible obs: 97.2 % / Redundancy: 13.3 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 41.59 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 8.64 / Num. unique obs: 2393 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.086 / Rrim(I) all: 0.312 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 16.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→31.26 Å
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Refine LS restraints |
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LS refinement shell |
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