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Yorodumi- PDB-4ore: Cyrstal structure of O-acetylserine sulfhydrylase ternary complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ore | ||||||
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Title | Cyrstal structure of O-acetylserine sulfhydrylase ternary complex from Haemophilus influenzae at 2.2 A | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Alpha/beta fold / Pyridoxal phosphate Co-factor / cysteine synthase/cystathionine beta-synthase family / cysteine synthase activity / 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kaushik, A. / Ekka, M.K. / Singh, A.K. / Kumaran, S. | ||||||
Citation | Journal: To be Published Title: Cyrstal structure of O-acetylserine sulfhydrylase ternary complex from Haemophilus influenzae at 2.2 A Authors: Kaushik, A. / Ekka, M.K. / Singh, A.K. / Kumaran, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ore.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ore.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ore.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/4ore ftp://data.pdbj.org/pub/pdb/validation_reports/or/4ore | HTTPS FTP |
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-Related structure data
Related structure data | 4ho1S S: Starting model for refinement |
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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: 35598.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: IPTG inducible / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC51907 / Gene: cysK, HI_1103 / Plasmid: pET 28A / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P45040, cysteine synthase |
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#2: Protein/peptide | Mass: 900.930 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-OAS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 1.3M sodium Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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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 29, 2013 |
Radiation | Monochromator: Graphite polar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→39.676 Å / Num. obs: 22189 / % possible obs: 13 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HO1 Resolution: 2.2→39.676 Å / SU ML: 0.36 / Isotropic thermal model: Isotropic Model / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 30.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.11 Å2 / ksol: 0.395 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→39.676 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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