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Yorodumi- PDB-7yol: Crystal structure of tetra mutant (D67E, A68P, L98I, A301S) of O-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yol | ||||||
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Title | Crystal structure of tetra mutant (D67E, A68P, L98I, A301S) of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide of serine acetyltransferase from Haemophilus influenzae at 2.4 A | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Tetra mutant (D67E / A68P / L98I / A301S) / O-acetylserine sulfhydrylase / Haemophilus influenzae / high-affinity inhibitory peptide of serine acetyltransferase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process from serine / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae Rd KW20 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Saini, N. / Kumar, N. / Rahisuddin, R. / Singh, A.K. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of tetra mutant (D67E, A68P, L98I, A301S) of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine ...Title: Crystal structure of tetra mutant (D67E, A68P, L98I, A301S) of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Haemophilus influenzae at 2.4 A Authors: Kumar, N. / Rahisuddin, R. / Saini, N. / Singh, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yol.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yol.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/7yol ftp://data.pdbj.org/pub/pdb/validation_reports/yo/7yol | HTTPS FTP |
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-Related structure data
Related structure data | 1y7lS 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: 33707.527 Da / Num. of mol.: 1 / Mutation: D67E, A68P, L98I, A301S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria) Gene: cysK, HI_1103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45040, cysteine synthase |
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#2: Protein/peptide | Mass: 775.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae Rd KW20 (bacteria) / References: UniProt: P43886 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.76 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 1.3M Sodium Citrate / PH range: 7.3-7.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 29, 2012 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.33 Å / Num. obs: 11361 / % possible obs: 99.54 % / Redundancy: 15.5 % / CC1/2: 0.886 / CC star: 0.969 / Net I/σ(I): 126.45 |
Reflection shell | Resolution: 2.5→2.589 Å / Num. unique obs: 970 / CC1/2: 0.835 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y7L Resolution: 2.4→42.33 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.489 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.579 / ESU R Free: 0.227 Details: Hydrogens have been used if present in the input file
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.251 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→42.33 Å
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Refine LS restraints |
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LS refinement shell |
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