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Yorodumi- PDB-4zu1: Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zu1 | ||||||||||||
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Title | Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilus influenzae in complex with O-acetyl serine and peptide inhibitor | ||||||||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Amino-acid biosynthesis / Cysteine biosynthesis / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Haemophilus influenzae KW20 (bacteria) Salmonella typhimurium LT2 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.202 Å | ||||||||||||
Authors | Ekka, M.K. / Singh, A.K. / Kaushik, A. / Kumaran, S. | ||||||||||||
Citation | Journal: To Be Published Title: Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilus inuen-zae in complex with O-acetyl serine and peptide inhibitor Authors: Ekka, M.K. / Singh, A.K. / Kaushik, A. / Kumaran, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zu1.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zu1.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/4zu1 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zu1 | 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: 35460.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae KW20 (bacteria) / Strain: KW20 / Gene: cysK, HI_1103 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45040, cysteine synthase |
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#2: Protein/peptide | Mass: 1177.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Salmonella typhimurium LT2 (bacteria) / References: UniProt: P29847 |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-OAS / |
#5: 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: 2.02 Å3/Da / Density % sol: 34.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: o.1 M HEPES 1.2M Sodium Citrate / PH range: 7.4-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 13806 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 32.9 |
Reflection shell | Highest resolution: 2.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.71 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HO1 Resolution: 2.202→30 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.55 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.202→30 Å
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Refine LS restraints |
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LS refinement shell |
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