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Yorodumi- PDB-7xrq: The Catalytic Core Structure of Cystathionine beta-Synthase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xrq | |||||||||
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Title | The Catalytic Core Structure of Cystathionine beta-Synthase from Candida albicans | |||||||||
Components | Cystathionine beta-synthaseCystathionine beta synthase | |||||||||
Keywords | LYASE / Cystathionine beta-synthase / Catalytic core center | |||||||||
Function / homology | Function and homology information cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / traversing start control point of mitotic cell cycle / cysteine biosynthetic process from serine / transsulfuration / cytoplasm Similarity search - Function | |||||||||
Biological species | Candida albicans (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | |||||||||
Authors | Lou, H.X. / Yu, H.N. / Chang, W.Q. | |||||||||
Funding support | China, 2items
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Citation | Journal: Sci Adv / Year: 2022 Title: Inhibition of fungal pathogenicity by targeting the H 2 S-synthesizing enzyme cystathionine beta-synthase. Authors: Chang, W. / Zhang, M. / Jin, X. / Zhang, H. / Zheng, H. / Zheng, S. / Qiao, Y. / Yu, H. / Sun, B. / Hou, X. / Lou, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xrq.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xrq.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/7xrq ftp://data.pdbj.org/pub/pdb/validation_reports/xr/7xrq | HTTPS FTP |
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-Related structure data
Related structure data | 4cooS 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
#1: Protein | Mass: 38267.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: CYS4, orf19.4536, CAALFM_C101870CA / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59T95, cystathionine beta-synthase #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.11 Å3/Da / Density % sol: 41.82 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 / Details: 1.8 M ammonium citrate tribasic, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 22086 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Rsym value: 0.05 / Χ2: 0.997 / Net I/σ(I): 36.33 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1104 / CC1/2: 0.932 / Rpim(I) all: 0.242 / Rrim(I) all: 0.636 / Rsym value: 0.588 / Χ2: 0.968 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4COO Resolution: 2.501→49.01 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→49.01 Å
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Refine LS restraints |
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LS refinement shell |
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