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Yorodumi- PDB-8he6: Crystal structure of a fosfomycin and bleomycin resistant protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8he6 | |||||||||
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Title | Crystal structure of a fosfomycin and bleomycin resistant protein (ALL3014) from Anabaena/Nostoc cyanobacterium at 1.70 A resolution | |||||||||
Components | All3014 protein | |||||||||
Keywords | TRANSFERASE / All3014 protein | |||||||||
Function / homology | Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / All3014 protein Function and homology information | |||||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Chatterjee, A. / Singh, P.K. / Singh, T.P. / Marina, A. / Sharma, S. / Rai, L.C. | |||||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of a fosfomycin and bleomycin resistant protein (ALL3014) from Anabaena/Nostoc cyanobacterium at 1.70 A resolution Authors: Chatterjee, A. / Singh, P.K. / Singh, T.P. / Marina, A. / Sharma, S. / Rai, L.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8he6.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8he6.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 8he6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8he6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8he6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8he6_validation.xml.gz | 14 KB | Display | |
Data in CIF | 8he6_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/8he6 ftp://data.pdbj.org/pub/pdb/validation_reports/he/8he6 | HTTPS FTP |
-Related structure data
Related structure data | 6a4xS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains A B) |
-Components
#1: Protein | Mass: 13658.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all3014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YSS0 #2: Chemical | ChemComp-CA / | #3: Chemical | ChemComp-MG / | #4: 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: 2.55 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2M lithium sulphate, 0.1M sodium acetate, 50 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0718 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 2016 / Details: mirror |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0718 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→77.41 Å / Num. obs: 31802 / % possible obs: 95 % / Redundancy: 9.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Rsym value: 0.072 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1753 / CC1/2: 0.62 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A4X Resolution: 1.7→48.953 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.183 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.107 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: 27.792 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→48.953 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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