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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 | |||||||||
Components | Cystathionine gamma-synthase homolog | |||||||||
Keywords | LYASE / CGL / PLP / MccB | |||||||||
| Function / homology | Function and homology informationcystathionine 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 | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Ha, N.-C. / Lee, D. / Lee, H. / Byun, K. | |||||||||
| Funding support | Korea, Republic Of, 2items
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Citation | Journal: To Be PublishedTitle: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9j7q.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9j7q.ent.gz | 67.7 KB | Display | PDB format |
| PDBx/mmJSON format | 9j7q.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9j7q_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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| Full document | 9j7q_full_validation.pdf.gz | 452.7 KB | Display | |
| Data in XML | 9j7q_validation.xml.gz | 20.2 KB | Display | |
| Data in CIF | 9j7q_validation.cif.gz | 28.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/9j7q ftp://data.pdbj.org/pub/pdb/validation_reports/j7/9j7q | HTTPS FTP |
-Related structure data
| Related structure data | |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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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.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
| 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: MOLECULAR REPLACEMENT / Resolution: 1.64→31.26 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7379 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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About Yorodumi




Staphylococcus aureus subsp. aureus Mu50 (bacteria)
X-RAY DIFFRACTION
Korea, Republic Of, 2items
Citation
PDBj



