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Yorodumi- PDB-5dbh: Crystal structure of O-acetylserine sulfhydrylase from haemophilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dbh | |||||||||
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Title | Crystal structure of O-acetylserine sulfhydrylase from haemophilus influenzae in complex with reaction intermediate alpha-aminoacrylate | |||||||||
Components | Cysteine synthase | |||||||||
Keywords | TRANSFERASE / cysteine synthase activity / transferase activity | |||||||||
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: 1.98 Å | |||||||||
Authors | Kaushik, A. / Ekka, M.K. / Singh, A.K. / Kumaran, S. | |||||||||
Citation | Journal: To Be Published Title: Crystal structure of O-acetylserine sulfhydrylase from haemophilus influenzae in complex with reaction intermediate alpha-aminoacrylate 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 | 5dbh.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dbh.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/5dbh ftp://data.pdbj.org/pub/pdb/validation_reports/db/5dbh | 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: 34252.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Cell: bacteria / Cell line: Bacterial cells / Gene: cysK, HI_1103 / Plasmid: pET28A / Details (production host): N terminal His tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45040, cysteine synthase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-0JO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 38.77 % / Description: TRINGLE SHAPED CRYSTAL (PRISIM FROM THE TOP) |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 7.5 / Details: 0.1MHEPES 1.3M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2012 / Details: varimax optics |
Radiation | Monochromator: Graphite polar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→32 Å / Num. obs: 19145 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 53 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 22 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HO1 Resolution: 1.98→32 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.33 / 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: 1.98→32 Å
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Refine LS restraints |
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LS refinement shell |
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