+Open data
-Basic information
Entry | Database: PDB / ID: 8stw | ||||||
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Title | K384N HUMAN CYSTATHIONINE BETA-SYNTHASE (delta 411-551) | ||||||
Components | Cystathionine beta-synthase, K384N variantCystathionine beta synthase | ||||||
Keywords | LYASE / PLP / Heme / hydrogen sulfide | ||||||
Function / homology | Function and homology information Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / cystathionine beta-synthase activity / carbon monoxide binding / hydrogen sulfide biosynthetic process ...Cysteine formation from homocysteine / homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / Metabolism of ingested SeMet, Sec, MeSec into H2Se / homocysteine metabolic process / cystathionine beta-synthase activity / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine metabolic process / cartilage development involved in endochondral bone morphogenesis / L-serine catabolic process / regulation of nitric oxide mediated signal transduction / L-cysteine catabolic process / cysteine biosynthetic process / cerebellum morphogenesis / nitric oxide binding / cysteine biosynthetic process from serine / DNA protection / transsulfuration / endochondral ossification / S-adenosyl-L-methionine binding / response to folic acid / nitrite reductase (NO-forming) activity / superoxide metabolic process / maternal process involved in female pregnancy / blood vessel remodeling / blood vessel diameter maintenance / oxygen binding / pyridoxal phosphate binding / cellular response to hypoxia / ubiquitin protein ligase binding / heme binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Mascarenhas, R. / Roman, J. / Banerjee, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Disease-causing cystathionine beta-synthase linker mutations impair allosteric regulation. Authors: Roman, J.V. / Mascarenhas, R. / Ceric, K. / Ballou, D.P. / Banerjee, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8stw.cif.gz | 410 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8stw.ent.gz | 335.1 KB | Display | PDB format |
PDBx/mmJSON format | 8stw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/8stw ftp://data.pdbj.org/pub/pdb/validation_reports/st/8stw | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 39907.648 Da / Num. of mol.: 6 / Mutation: K384N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35520, cystathionine beta-synthase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-HEM / #4: 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: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22 % PEG 3,350, 6 % Tacsimate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.976 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43.11 Å / Num. obs: 100667 / % possible obs: 93.3 % / Redundancy: 3.8 % / CC1/2: 0.997 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.4→2.44 Å / Num. unique obs: 5138 / CC1/2: 0.933 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.792 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.643 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→43.11 Å
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