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Yorodumi- PDB-7c35: Crystal structure of M96A mutant of O-acetyl-L-serine sulfhydryla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c35 | ||||||
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Title | Crystal structure of M96A mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae | ||||||
Components | Cysteine synthase | ||||||
Keywords | TRANSFERASE / PLP dependent enzyme / Cysteine metabolizing Enzyme / O acetyl transferase enzyme | ||||||
Function / homology | Function and homology information cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae Rd KW20 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Abhishek, K. / Rahisuddin, R. / Kumaran, S. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Molecular mechanism of selective substrate engagement and inhibitor disengagement of cysteine synthase. Authors: Kaushik, A. / Rahisuddin, R. / Saini, N. / Singh, R.P. / Kaur, R. / Koul, S. / Kumaran, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c35.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c35.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 7c35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/7c35 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/7c35 | HTTPS FTP |
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-Related structure data
Related structure data | 5xcnC 5xcpC 5xcwC 7cm8C 4ho1S 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
#1: Protein | Mass: 37144.273 Da / Num. of mol.: 1 / Mutation: M96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria) Gene: cysK, HI_1103 / Plasmid: pET28a+ Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P45040, cysteine synthase |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM Hepes buffer pH 7.4, 1.4M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2013 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35.762 Å / Num. obs: 16477 / % possible obs: 99.52 % / Redundancy: 3.9 % / Biso Wilson estimate: 32.28 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.087 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.01 / Num. unique obs: 2379 / CC1/2: 0.866 / CC star: 0.963 / Rrim(I) all: 0.315 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HO1 Resolution: 2.1→35.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
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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 max: 99.18 Å2 / Biso mean: 37.7276 Å2 / Biso min: 18.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→35.74 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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