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- PDB-8k06: Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thali... -

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Basic information

Entry
Database: PDB / ID: 8k06
TitlePseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- PSU, R5P bound K185A mutant
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'-MONOPHOSPHATE / 5-O-phosphono-beta-D-ribofuranose / Pseudouridine-5'-phosphate glycosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,4159
Polymers108,3723
Non-polymers1,0436
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-61 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.560, 105.838, 73.555
Angle α, β, γ (deg.)90.00, 118.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36123.988 Da / Num. of mol.: 3 / Mutation: K185A
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.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PSU / PSEUDOURIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE / 5-O-phosphono-beta-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Lithium sulfate, 0.1M MES pH 6, 20% (w/v) PEG 4000

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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: May 29, 2023
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.845→50 Å / Num. obs: 81648 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.973 / CC star: 0.993 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.089 / Rrim(I) all: 0.164 / Χ2: 1.667 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.86-1.933.51.10981700.490.8110.6981.3141.03899.9
1.93-23.50.71582120.6810.90.4520.8481.167100
2-2.093.50.47782280.7840.9370.3010.5651.357100
2.09-2.213.50.34682340.8630.9630.2180.411.575100
2.21-2.343.50.27982310.9080.9760.1760.331.72399.9
2.34-2.523.50.22882120.9380.9840.1430.271.85199.9
2.52-2.783.60.17782390.9580.9890.1110.2092.00499.9
2.78-3.183.60.13482500.9710.9930.0840.1592.13399.9
3.18-4.013.50.09782000.9790.9950.0630.1161.94999
4.01-503.10.08676720.9750.9940.060.1051.88491.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v717data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.845→29.922 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 2033 2.49 %
Rwork0.1825 --
obs0.1831 81503 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.845→29.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 59 646 7403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096846
X-RAY DIFFRACTIONf_angle_d1.1979311
X-RAY DIFFRACTIONf_dihedral_angle_d11.6752475
X-RAY DIFFRACTIONf_chiral_restr0.0531141
X-RAY DIFFRACTIONf_plane_restr0.0061207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8453-1.88820.25521180.22424320X-RAY DIFFRACTION80
1.8882-1.93550.23071400.21185355X-RAY DIFFRACTION99
1.9355-1.98780.23541310.20385409X-RAY DIFFRACTION100
1.9878-2.04630.26411250.20015410X-RAY DIFFRACTION100
2.0463-2.11230.2271400.18865429X-RAY DIFFRACTION100
2.1123-2.18780.22121410.18715406X-RAY DIFFRACTION100
2.1878-2.27530.21651310.18235395X-RAY DIFFRACTION100
2.2753-2.37880.19031400.1855418X-RAY DIFFRACTION100
2.3788-2.50420.21351430.18795403X-RAY DIFFRACTION100
2.5042-2.6610.23221290.18625425X-RAY DIFFRACTION100
2.661-2.86630.22611350.18765445X-RAY DIFFRACTION100
2.8663-3.15450.20471420.1835408X-RAY DIFFRACTION100
3.1545-3.61030.20141420.17625408X-RAY DIFFRACTION99
3.6103-4.5460.19331410.16015309X-RAY DIFFRACTION97
4.546-29.9220.19451350.19034930X-RAY DIFFRACTION89

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