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- PDB-7w2i: Crystal structure of LOG (Rv1205) from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7w2i
TitleCrystal structure of LOG (Rv1205) from Mycobacterium tuberculosis
Components(Cytokinin riboside 5'-monophosphate ...) x 2
KeywordsHYDROLASE / LOG / Rv1205 / Mycobacterium tuberculosis
Function / homology: / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / cytokinin biosynthetic process / LOG family / Possible lysine decarboxylase / hydrolase activity / DI(HYDROXYETHYL)ETHER / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShang, L. / Zhang, G.
Funding support1items
OrganizationGrant numberCountry
Other government2019B1515120041
CitationJournal: 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
DepositionNov 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
D: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,15314
Polymers76,6094
Non-polymers54410
Water13,079726
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.958, 75.976, 134.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Cytokinin riboside 5'-monophosphate ... , 2 types, 4 molecules ABCD

#1: Protein Cytokinin riboside 5'-monophosphate phosphoribohydrolase


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
#2: Protein Cytokinin riboside 5'-monophosphate phosphoribohydrolase


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

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Non-polymers , 5 types, 736 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.8→1.85 Å / Num. unique obs: 3650 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qua

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 3276 5 %RANDOM
Rwork0.1652 ---
obs0.1677 61925 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.52 Å2 / Biso mean: 18.923 Å2 / Biso min: 5.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.62 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 1.8→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5383 0 33 726 6142
Biso mean--43.49 31.8 -
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135558
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155154
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.6247597
X-RAY DIFFRACTIONr_angle_other_deg1.4491.57611834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77421.811254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9031532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021226
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 243 -
Rwork0.258 4344 -
all-4587 -
obs--95.9 %

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