+Open data
-Basic information
Entry | Database: PDB / ID: 5its | ||||||
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Title | Crystal structure of LOG from Corynebacterium glutamicum | ||||||
Components | Cytokinin riboside 5'-monophosphate phosphoribohydrolase | ||||||
Keywords | HYDROLASE / Rossmann fold / nucleotide-binding domain / phosphoribohydrolase | ||||||
Function / homology | Function and homology information cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Seo, H.-G. / Kim, K.-J. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural basis for cytokinin production by LOG from Corynebacterium glutamicum Authors: Seo, H.-G. / Kim, S. / Sagong, H.Y. / Son, H.F. / Jin, K.S. / Kim, I.K. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5its.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5its.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 5its.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5its_validation.pdf.gz | 477.1 KB | Display | wwPDB validaton report |
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Full document | 5its_full_validation.pdf.gz | 483.1 KB | Display | |
Data in XML | 5its_validation.xml.gz | 30 KB | Display | |
Data in CIF | 5its_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/5its ftp://data.pdbj.org/pub/pdb/validation_reports/it/5its | HTTPS FTP |
-Related structure data
Related structure data | 2a33S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22581.900 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria) Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: Cgl2379 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8NN34, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: Chemical | #3: Chemical | ChemComp-GOL / #4: 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: 3.06 Å3/Da / Density % sol: 59.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, DL-malic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2014 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→95.62 Å / Num. obs: 44133 / % possible obs: 95.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.5 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A33 Resolution: 2.3→95.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.513 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 95.95 Å2 / Biso mean: 29.687 Å2 / Biso min: 12.12 Å2
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Refinement step | Cycle: final / Resolution: 2.3→95.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.303→2.363 Å / Total num. of bins used: 20
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