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Yorodumi- PDB-9f14: The crystal structure of full length tetramer CysB from Klebsiell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9f14 | ||||||
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Title | The crystal structure of full length tetramer CysB from Klebsiella aerogenes in complex with N-acetylserine | ||||||
Components | HTH-type transcriptional regulator CysB | ||||||
Keywords | TRANSCRIPTION / CysB / cysteine biosynthesis / LysR family / transcriptional regulator | ||||||
Function / homology | Function and homology information cysteine biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm Similarity search - Function | ||||||
Biological species | Klebsiella aerogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Verschueren, K.H.G. / Dodson, E.J. / Wilkinson, A.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Eur.Biophys.J. / Year: 2024 Title: The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine. Authors: Verschueren, K.H.G. / Dodson, E.J. / Wilkinson, A.J. #1: Journal: Structure / Year: 1997 Title: The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement. Authors: Tyrrell, R. / Verschueren, K.H. / Dodson, E.J. / Murshudov, G.N. / Addy, C. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f14.cif.gz | 247.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f14.ent.gz | 204.6 KB | Display | PDB format |
PDBx/mmJSON format | 9f14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f14_validation.pdf.gz | 1014.4 KB | Display | wwPDB validaton report |
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Full document | 9f14_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 9f14_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 9f14_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/9f14 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/9f14 | HTTPS FTP |
-Related structure data
Related structure data | 9fddC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 36008.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: cysB / Plasmid: pKKCysB / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P45600 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 53 % / Description: Chunky |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 12 -17% PEG 8000, 0.2M sodium tartrate and 0.1M Tris-HCl pH 8.5, 0.2M KSCN, 10 mM N-acetylserine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 1998 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→19.817 Å / Num. obs: 33205 / % possible obs: 99.8 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Net I/σ(I): 20 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.817 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.314 / WRfactor Rwork: 0.236 / Average fsc free: 0.935 / Average fsc work: 0.9665 / Cross valid method: FREE R-VALUE / ESU R: 0.357 / ESU R Free: 0.279 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.806 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.817 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: 20
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