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- PDB-5wq3: Crystal structure of type-II LOG from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5wq3
TitleCrystal structure of type-II LOG from Corynebacterium glutamicum
ComponentsCytokinin riboside 5'-monophosphate phosphoribohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process
Similarity search - Function
: / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / : / Cytokinin riboside 5'-monophosphate phosphoribohydrolase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeo, H. / Kim, K.-J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for a novel type of cytokinin-activating protein
Authors: Seo, H. / Kim, K.-J.
History
DepositionNov 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 16, 2020Group: Derived calculations / Structure summary / Category: pdbx_struct_special_symmetry / struct / Item: _struct.title
Revision 1.3Nov 8, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,39816
Polymers89,3973
Non-polymers1,00113
Water4,396244
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

C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules

C: Cytokinin riboside 5'-monophosphate phosphoribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,79632
Polymers178,7946
Non-polymers2,00226
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area21950 Å2
ΔGint-245 kcal/mol
Surface area47570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.701, 173.623, 79.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

1PE

21C-304-

CL

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Cytokinin riboside 5'-monophosphate phosphoribohydrolase


Mass: 29798.986 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cg1261 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1B4WK77, UniProt: Q8NRE2*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 7 types, 257 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.91 Å3/Da / Density % sol: 35.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: PEG 3350, Lithium chloride

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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: Nov 22, 2014
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: 1.95→50 Å / Num. obs: 47969 / % possible obs: 95.5 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 39
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.46 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WEK

1wek


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.368 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 2296 4.8 %RANDOM
Rwork0.1778 ---
obs0.1801 45666 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.03 Å2 / Biso mean: 32.901 Å2 / Biso min: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å2-0 Å2
2--1.68 Å20 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 45 244 5143
Biso mean--46.32 36.59 -
Num. residues----620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195194
X-RAY DIFFRACTIONr_bond_other_d0.0010.024933
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9537042
X-RAY DIFFRACTIONr_angle_other_deg0.891311339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64123.891239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34315827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1941526
X-RAY DIFFRACTIONr_chiral_restr0.1120.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215936
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021234
LS refinement shellResolution: 1.951→2.002 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 166 -
Rwork0.302 3127 -
all-3293 -
obs--90.37 %

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