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- PDB-5zi9: Crystal structure of type-II LOG from Streptomyces coelicolor A3 -

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Basic information

Entry
Database: PDB / ID: 5zi9
TitleCrystal structure of type-II LOG from Streptomyces coelicolor A3
ComponentsCytokinin riboside 5'-monophosphate phosphoribohydrolase
KeywordsHYDROLASE
Function / homologycytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / cytokinin biosynthetic process / LOG family / Possible lysine decarboxylase / cytosol / CITRATE ANION / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeo, H. / Kim, K.-J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural and biochemical characterization of the type-II LOG protein from Streptomyces coelicolor A3.
Authors: Seo, H. / Kim, K.J.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Sep 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)116,20922
Polymers114,2104
Non-polymers2,00018
Water1,24369
1
A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules

A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules

A: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,31433
Polymers171,3156
Non-polymers2,99927
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area38300 Å2
ΔGint-116 kcal/mol
Surface area44460 Å2
MethodPISA
2
C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
D: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules

C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
D: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules

C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
D: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,31433
Polymers171,3156
Non-polymers2,99927
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area36960 Å2
ΔGint-122 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.768, 206.768, 206.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-617-

HOH

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Components

#1: Protein
Cytokinin riboside 5'-monophosphate phosphoribohydrolase


Mass: 28552.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO5140 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9FBL8, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Polyethylene glycol 3350, citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 27, 2016
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→146.21 Å / Num. obs: 49440 / % possible obs: 98 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.67
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2396 / CC1/2: 0.374 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQ3

5wq3


Resolution: 2.5→146.21 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.666 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 2394 4.8 %RANDOM
Rwork0.1847 ---
obs0.1872 47036 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 32.075 Å2 / Biso min: 16.37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.5→146.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6900 0 134 69 7103
Biso mean--40.77 32.84 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197222
X-RAY DIFFRACTIONr_bond_other_d0.0020.026804
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9829786
X-RAY DIFFRACTIONr_angle_other_deg1.078315688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90923.354316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.83151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9541554
X-RAY DIFFRACTIONr_chiral_restr0.0960.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218118
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021552
LS refinement shellResolution: 2.505→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 188 -
Rwork0.327 3405 -
all-3593 -
obs--96.66 %

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