+Open data
-Basic information
Entry | Database: PDB / ID: 2gff | ||||||
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Title | Crystal Structure of Yersinia pestis LsrG | ||||||
Components | LsrG Protein | ||||||
Keywords | SUGAR BINDING PROTEIN / dimeric alpha+beta barrel Ferredoxin fold | ||||||
Function / homology | Function and homology information (4S)-4-hydroxy-5-phosphooxypentane-2,3-dione isomerase / intramolecular oxidoreductase activity, interconverting aldoses and ketoses / catalytic activity / oxidoreductase activity / cytosol Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | de Carvalho-Kavanagh, M. / Schafer, J. / Lekin, T. / Toppani, D. / Chain, P. / Lao, V. / Motin, V. / Garcia, E. / Segelke, B. | ||||||
Citation | Journal: To be Published Title: Crystal structure of lsrG from Yersinia Pestis Authors: de Carvalho-Kavanagh, M. / Schafer, J. / Lekin, T. / Toppani, D. / Coleman, M. / Chain, P. / Lao, V. / Zemla, A. / Motin, V. / Garcia, E. / Segelke, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gff.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gff.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gff_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 2gff_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 2gff_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 2gff_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/2gff ftp://data.pdbj.org/pub/pdb/validation_reports/gf/2gff | HTTPS FTP |
-Related structure data
Similar structure data |
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-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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Details | Putative dimer unconfirmed related by NCS |
-Components
#1: Protein | Mass: 12469.794 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: D27 / Gene: lsrG / Plasmid: pETBlue-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 21960758, UniProt: Q7CG46*PLUS #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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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: 1.89 Å3/Da / Density % sol: 34.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 6K, 100 mM MES, 0.17 M ammonium sulfate 100 microliter reservoir, 800 nanoliter drop,intelliplate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 70 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97910, 0.97951, 0.97444 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2005 | ||||||||||||
Radiation | Monochromator: Liquid nitrogen cooled dual crystal silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. all: 20024 / Num. obs: 20024 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.077 / Net I/σ(I): 11.4 | ||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1949 / Rsym value: 0.68 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.144 / Stereochemistry target values: Engh & Huber
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.581 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→20 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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