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Yorodumi- PDB-4lmb: Crystal structure analysis of O-acetylserine sulfhydrylase CysK2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lmb | ||||||
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Title | Crystal structure analysis of O-acetylserine sulfhydrylase CysK2 complexed with cystine from Microcystis aeruginosa 7806 | ||||||
Components | Cysteine synthase | ||||||
Keywords | TRANSFERASE / sulfhydrylase | ||||||
Function / homology | Function and homology information cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine Similarity search - Function | ||||||
Biological species | Microcystis aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Lu, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Structural and biochemical analyses of Microcystis aeruginosa O-acetylserine sulfhydrylases reveal a negative feedback regulation of cysteine biosynthesis. Authors: Lu, M. / Xu, B.Y. / Zhou, K. / Cheng, W. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lmb.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lmb.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/4lmb ftp://data.pdbj.org/pub/pdb/validation_reports/lm/4lmb | HTTPS FTP |
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-Related structure data
Related structure data | 4lmaC 2q3bS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34744.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microcystis aeruginosa (bacteria) / Strain: PCC 7806 / Gene: cysK, IPF_2058, IPF_3084 / Production host: Escherichia coli (E. coli) / References: UniProt: A8YBP8, cysteine synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-PLP / | #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: 3.4 Å3/Da / Density % sol: 63.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5M (NH4)2SO4, 0.1M Bis-Tris-propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 36107 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q3B Resolution: 1.91→32.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.389 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→32.06 Å
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Refine LS restraints |
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