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Yorodumi- PDB-7w2i: Crystal structure of LOG (Rv1205) from Mycobacterium tuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w2i | ||||||
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Title | Crystal structure of LOG (Rv1205) from Mycobacterium tuberculosis | ||||||
Components | (Cytokinin riboside 5'-monophosphate ...) x 2 | ||||||
Keywords | HYDROLASE / LOG / Rv1205 / Mycobacterium tuberculosis | ||||||
Function / homology | cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / cytokinin biosynthetic process / LOG family / Possible lysine decarboxylase / DI(HYDROXYETHYL)ETHER / Cytokinin riboside 5'-monophosphate phosphoribohydrolase Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shang, L. / Zhang, G. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Crystal structure of the cytokinin-producing enzyme "lonely guy" (LOG) from Mycobacterium tuberculosis. Authors: Shang, L. / Li, G. / Lin, Q. / Ou, M. / Liang, J. / Xiao, G. / Wang, Z. / Cui, S. / Zhang, T. / Liu, L. / Zhang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w2i.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w2i.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 7w2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w2i_validation.pdf.gz | 482.5 KB | Display | wwPDB validaton report |
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Full document | 7w2i_full_validation.pdf.gz | 485.5 KB | Display | |
Data in XML | 7w2i_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 7w2i_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/7w2i ftp://data.pdbj.org/pub/pdb/validation_reports/w2/7w2i | HTTPS FTP |
-Related structure data
Related structure data | 3quaS 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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-Components
-Cytokinin riboside 5'-monophosphate ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 19613.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377, ERS027646_02317, ERS027661_02284, FPJ30_ ...Gene: yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377, ERS027646_02317, ERS027661_02284, FPJ30_06615, FPJ31_06635, FPJ32_06600, FPJ33_06635, FPJ34_06605, FPJ35_06645, FPJ36_06610, FPJ37_06625, FPJ38_06685, FPJ39_06605, FPJ40_06630, FPJ41_06610, FPJ42_06600, FPJ43_06625, FPJ44_06630, FPJ45_06605, FPJ46_06605, FPJ47_06620, FPJ48_06590, FPJ49_06625, FPJ50_06605, FPJ51_06600, FPJ52_06615, FPJ53_06605, FPJ54_06615, FPJ55_06630, FPJ56_06605, FPJ57_06600, FPJ58_06625, FPJ59_06615, FPJ60_06630, FPJ61_06605, FPJ62_06605, FPJ63_06620, FPJ64_06630, FPJ65_06615, FPJ66_06605, FPJ67_06650, FPJ69_06650, FPJ70_06650, FPJ71_06650, FPJ72_05390, FPJ73_06605, FPJ76_06570, FPJ77_06635, FPJ78_06620, FPJ79_06645, FPJ80_06625, FPJ81_06635, FPJ82_06640, FPJ83_14970, FPJ84_06625, FPJ85_14960, FPJ86_14950, FPJ87_14955, FPJ88_06580, FPJ89_06625, FPJ90_06600, FPJ91_06645, FPJ92_06600, FPJ93_06635, FPJ94_05385, FPJ95_06625, FPJ96_06640, FPJ97_06645, FPJ98_06615, FPJ99_06640, FPK00_06610, FPK01_06670, FPK02_06615, FPK03_06630, FPK04_06630, FPK05_06625, FPK06_06610, FPK07_06620, FPK08_06630, FPK09_06625, FPK10_05385, FPK11_06625, FPK12_06590, FPK13_06620, FPK14_06625, FPK16_06620, FPK17_06620, FPK18_06620, FPK19_06635, FPK20_06635, FPK21_06605, FPK22_06630, HRD52_06340, HRD53_06340, SAMEA2683035_01466 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A045J166, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: Protein | Mass: 18998.580 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377, ERS027646_02317, ERS027661_02284, FPJ30_ ...Gene: yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377, ERS027646_02317, ERS027661_02284, FPJ30_06615, FPJ31_06635, FPJ32_06600, FPJ33_06635, FPJ34_06605, FPJ35_06645, FPJ36_06610, FPJ37_06625, FPJ38_06685, FPJ39_06605, FPJ40_06630, FPJ41_06610, FPJ42_06600, FPJ43_06625, FPJ44_06630, FPJ45_06605, FPJ46_06605, FPJ47_06620, FPJ48_06590, FPJ49_06625, FPJ50_06605, FPJ51_06600, FPJ52_06615, FPJ53_06605, FPJ54_06615, FPJ55_06630, FPJ56_06605, FPJ57_06600, FPJ58_06625, FPJ59_06615, FPJ60_06630, FPJ61_06605, FPJ62_06605, FPJ63_06620, FPJ64_06630, FPJ65_06615, FPJ66_06605, FPJ67_06650, FPJ69_06650, FPJ70_06650, FPJ71_06650, FPJ72_05390, FPJ73_06605, FPJ76_06570, FPJ77_06635, FPJ78_06620, FPJ79_06645, FPJ80_06625, FPJ81_06635, FPJ82_06640, FPJ83_14970, FPJ84_06625, FPJ85_14960, FPJ86_14950, FPJ87_14955, FPJ88_06580, FPJ89_06625, FPJ90_06600, FPJ91_06645, FPJ92_06600, FPJ93_06635, FPJ94_05385, FPJ95_06625, FPJ96_06640, FPJ97_06645, FPJ98_06615, FPJ99_06640, FPK00_06610, FPK01_06670, FPK02_06615, FPK03_06630, FPK04_06630, FPK05_06625, FPK06_06610, FPK07_06620, FPK08_06630, FPK09_06625, FPK10_05385, FPK11_06625, FPK12_06590, FPK13_06620, FPK14_06625, FPK16_06620, FPK17_06620, FPK18_06620, FPK19_06635, FPK20_06635, FPK21_06605, FPK22_06630, HRD52_06340, HRD53_06340, SAMEA2683035_01466 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A045J166, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
-Non-polymers , 5 types, 736 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.93 Å / Num. obs: 65281 / % possible obs: 99.6 % / Redundancy: 9.8 % / CC1/2: 0.997 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.8→1.85 Å / Num. unique obs: 3650 / CC1/2: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3qua Resolution: 1.8→47.93 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.698 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 / 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: 73.52 Å2 / Biso mean: 18.923 Å2 / Biso min: 5.69 Å2
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Refinement step | Cycle: final / Resolution: 1.8→47.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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