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Yorodumi- PDB-6khq: bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6khq | ||||||
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Title | bacterial cystathionine gamma-lyase MccB of Staphylococcus aureus with cofactor PLP | ||||||
Components | Cystathionine gamma lyase | ||||||
Keywords | LYASE / Cystathionine gamma lyase / CGL / MccB / yhrB / PLP / Pyridoxal Phosphate / Cysteine synthesis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ha, N.-C. / Lee, D. | ||||||
Citation | Journal: Crystals / Year: 2019 Title: Crystal Structure of Bacterial Cystathionine Gamma-Lyase in The Cysteine Biosynthesis Pathway of Staphylococcus aureus Authors: Lee, D. / Jeong, S. / Ahn, J. / Ha, N.-C. / Kwon, A.-R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6khq.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6khq.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 6khq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/6khq ftp://data.pdbj.org/pub/pdb/validation_reports/kh/6khq | HTTPS FTP |
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-Related structure data
Related structure data | 6kgzSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 43565.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Strain: Mu50 / Gene: yrhB, SAV0460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3JQ19, cystathionine gamma-lyase #2: Water | ChemComp-HOH / | 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: 2.65 Å3/Da / Density % sol: 53.55 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 400, Sodium Acetate |
-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: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 39074 / % possible obs: 99.5 % / Redundancy: 14.1 % / Biso Wilson estimate: 26.43 Å2 / CC1/2: 1 / Rpim(I) all: 0.017 / Rrim(I) all: 0.072 / Net I/σ(I): 28.11 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.92 / Num. unique obs: 1914 / CC1/2: 0.701 / Rpim(I) all: 0.126 / Rrim(I) all: 0.373 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KGZ Resolution: 2.3→42.2 Å / SU ML: 0.2616 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.8161
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→42.2 Å
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Refine LS restraints |
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LS refinement shell |
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