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Yorodumi- PDB-3iqi: Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iqi | ||||||
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Title | Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide MNENI | ||||||
Components |
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Keywords | TRANSFERASE / PROTEIN-PEPTIDE COMPLEX / Allosteric enzyme / Amino-acid biosynthesis / Cysteine biosynthesis / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information cysteine synthase / 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: 1.7 Å | ||||||
Authors | Roderick, S.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Design of o-acetylserine sulfhydrylase inhibitors by mimicking nature. Authors: Salsi, E. / Bayden, A.S. / Spyrakis, F. / Amadasi, A. / Campanini, B. / Bettati, S. / Dodatko, T. / Cozzini, P. / Kellogg, G.E. / Cook, P.F. / Roderick, S.L. / Mozzarelli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iqi.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iqi.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 3iqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iqi ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iqi | HTTPS FTP |
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-Related structure data
Related structure data | 3iqgC 3iqhC 1y7lS 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: 33651.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: cysK, HI1103 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45040, cysteine synthase |
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#2: Protein/peptide | Mass: 619.688 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: 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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, Ammonium sulfate, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2009 |
Radiation | Monochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→22.08 Å / Num. all: 29196 / Num. obs: 29196 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 6.2 / Num. unique all: 3899 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y7L Resolution: 1.7→22.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.806 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.447 Å2
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Refine analyze | Luzzati coordinate error obs: 0.112 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→22.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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