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- PDB-8k05: Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thali... -

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Basic information

Entry
Database: PDB / ID: 8k05
TitlePseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- sulfate bound holoenzyme
ComponentsPseudouridine-5'-phosphate glycosidase
KeywordsHYDROLASE / metalloenzyme / glycosylase / C-nucleoside / pseudouridine monophosphate / METAL BINDING PROTEIN
Function / homology
Function and homology information


RNA glycosylase activity / pseudouridylate synthase / pseudouridylate synthase activity / peroxisome / metal ion binding
Similarity search - Function
Pseudouridine-5'-phosphate glycosidase / Indigoidine synthase A-like / Indigoidine synthase A like protein
Similarity search - Domain/homology
: / Pseudouridine-5'-phosphate glycosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLee, J.Y. / Kim, S.H. / Rhee, S.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C2092118 Korea, Republic Of
CitationJournal: Rna Biol. / Year: 2024
Title: Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana.
Authors: Lee, J. / Kim, S.H. / Rhee, S.
History
DepositionJul 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudouridine-5'-phosphate glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4294
Polymers36,1821
Non-polymers2473
Water5,405300
1
A: Pseudouridine-5'-phosphate glycosidase
hetero molecules

A: Pseudouridine-5'-phosphate glycosidase
hetero molecules

A: Pseudouridine-5'-phosphate glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,28712
Polymers108,5463
Non-polymers7419
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area7770 Å2
ΔGint-121 kcal/mol
Surface area34850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.126, 121.126, 121.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-709-

HOH

21A-734-

HOH

31A-793-

HOH

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Components

#1: Protein Pseudouridine-5'-phosphate glycosidase / PsiMP glycosidase / Pseudouridine monophosphate glycosidase


Mass: 36182.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PUMY, At1g50510, F11F12.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84K35, pseudouridylate synthase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Cacodylate pH6.5, 1.4M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 104528 / % possible obs: 99.9 % / Redundancy: 21.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.024 / Rrim(I) all: 0.113 / Χ2: 1.173 / Net I/σ(I): 6 / Num. measured all: 2288355
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.45-1.521.93.706103150.4550.7910.813.7941.07100
1.5-1.5621.92.46103990.6590.8910.5372.5181.092100
1.56-1.63221.639104240.8050.9450.3571.6771.096100
1.63-1.72221.042103640.9170.9780.2271.0661.102100
1.72-1.8322.10.665104330.9650.9910.1440.681.132100
1.83-1.9722.10.341104250.9890.9970.0740.3491.166100
1.97-2.1722.20.158104560.9970.9990.0340.1621.211100
2.17-2.4822.20.102104770.99810.0220.1041.212100
2.48-3.12220.068105480.99910.0150.0691.224100
3.12-5020.60.054106870.99910.0120.0551.43399.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→28.55 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 2000 1.92 %
Rwork0.2056 --
obs0.2058 104349 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 11 300 2571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062299
X-RAY DIFFRACTIONf_angle_d1.0593124
X-RAY DIFFRACTIONf_dihedral_angle_d12.588836
X-RAY DIFFRACTIONf_chiral_restr0.042380
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48580.32861410.31947257X-RAY DIFFRACTION100
1.4858-1.5260.30941430.29477265X-RAY DIFFRACTION100
1.526-1.57090.31321420.27777282X-RAY DIFFRACTION100
1.5709-1.62160.26711470.2697256X-RAY DIFFRACTION100
1.6216-1.67960.26531450.25397335X-RAY DIFFRACTION100
1.6796-1.74680.28931380.25287255X-RAY DIFFRACTION100
1.7468-1.82630.24821440.25167268X-RAY DIFFRACTION100
1.8263-1.92260.28211440.2537283X-RAY DIFFRACTION100
1.9226-2.0430.21411410.22087272X-RAY DIFFRACTION100
2.043-2.20070.23881430.20077345X-RAY DIFFRACTION100
2.2007-2.4220.21531420.20697304X-RAY DIFFRACTION100
2.422-2.77230.20311470.20997317X-RAY DIFFRACTION99
2.7723-3.49180.21211400.19147403X-RAY DIFFRACTION100
3.4918-28.550.17311430.16737507X-RAY DIFFRACTION99

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