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Yorodumi- PDB-7yod: Crystal structure of A68P single mutant of O-acetylserine sulfhyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yod | ||||||
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Title | Crystal structure of A68P single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.1 A | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / A68P single mutant / O-acetyl-L-serine sulfhydrylase / Haemophilus influenzae / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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) Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 Å | ||||||
Authors | Kumar, N. / Rahisuddin, R. / Saini, N. / Singh, A.K. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of A68P single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.1 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 | 7yod.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yod.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yod_validation.pdf.gz | 415.6 KB | Display | wwPDB validaton report |
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Full document | 7yod_full_validation.pdf.gz | 417 KB | Display | |
Data in XML | 7yod_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 7yod_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/7yod ftp://data.pdbj.org/pub/pdb/validation_reports/yo/7yod | HTTPS FTP |
-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: 33677.504 Da / Num. of mol.: 1 / Mutation: A68P 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: 900.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Salmonella typhimurium (bacteria) |
#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: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1M HEPES, 1.3M Sodium citrate / PH range: 7.3-7.9 |
-Data collection
Diffraction | Mean temperature: 293 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 26, 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: 2.101→39.81 Å / Num. obs: 16969 / % possible obs: 99.95 % / Redundancy: 1.1 % / Biso Wilson estimate: 32.49 Å2 / CC1/2: 1 / Net I/σ(I): 37.22 |
Reflection shell | Resolution: 2.101→2.176 Å / Num. unique obs: 1671 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y7L Resolution: 2.101→39.81 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.578 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.279 / ESU R Free: 0.208 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: 37.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.101→39.81 Å
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Refine LS restraints |
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LS refinement shell |
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