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- PDB-8k07: Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thali... -

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Basic information

Entry
Database: PDB / ID: 8k07
TitlePseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- citrate 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
CITRIC ACID / : / Pseudouridine-5'-phosphate glycosidase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.121 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)109,1139
Polymers108,3723
Non-polymers7416
Water14,574809
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-44 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.299, 68.518, 73.095
Angle α, β, γ (deg.)117.88, 94.31, 109.38
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Pseudouridine-5'-phosphate glycosidase / pseudouridine 5'-monophosphate glycosylase / ribose 5'-phosphate adduct / PsiMP glycosidase / ...pseudouridine 5'-monophosphate glycosylase / ribose 5'-phosphate adduct / 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Sodium citrate pH6.5, 16% PEG 10000

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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: 1.12→50 Å / Num. obs: 316141 / % possible obs: 92.4 % / Redundancy: 1.9 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.051 / Rrim(I) all: 0.072 / Χ2: 1.047 / Net I/σ(I): 6.5 / Num. measured all: 611922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.12-1.161.90.624281360.590.8610.6240.8820.86282.1
1.16-1.2120.529309000.6540.8890.5290.7481.09890.6
1.21-1.261.90.404312300.7590.9290.4040.5721.2491.1
1.26-1.3320.244315900.8790.9670.2440.3460.97992.3
1.33-1.4120.178318360.9270.9810.1780.2520.95693.2
1.41-1.5220.118321590.9640.9910.1180.1660.99194
1.52-1.6720.076324530.9820.9960.0760.1080.99194.9
1.67-1.921.90.052328250.9910.9980.0520.0730.95495.9
1.92-2.411.90.038331620.9940.9980.0380.0531.03197.1
2.41-501.90.037318500.9920.9980.0370.0531.37593

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.121→24.796 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 1987 0.63 %
Rwork0.2053 --
obs0.2053 316071 92.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.121→24.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6623 0 42 809 7474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066747
X-RAY DIFFRACTIONf_angle_d1.1539168
X-RAY DIFFRACTIONf_dihedral_angle_d13.9832458
X-RAY DIFFRACTIONf_chiral_restr0.0471117
X-RAY DIFFRACTIONf_plane_restr0.0061198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.121-1.14860.38191290.346418969X-RAY DIFFRACTION78
1.1486-1.17970.34811340.341921872X-RAY DIFFRACTION90
1.1797-1.21440.33141250.332422032X-RAY DIFFRACTION91
1.2144-1.25360.31961480.313722090X-RAY DIFFRACTION91
1.2536-1.29840.29221390.256122406X-RAY DIFFRACTION92
1.2984-1.35040.25581440.235222488X-RAY DIFFRACTION93
1.3504-1.41180.24741470.224822671X-RAY DIFFRACTION93
1.4118-1.48630.24831480.213922792X-RAY DIFFRACTION94
1.4863-1.57940.22481480.19622922X-RAY DIFFRACTION94
1.5794-1.70130.19511440.192323187X-RAY DIFFRACTION95
1.7013-1.87250.22221390.193323295X-RAY DIFFRACTION96
1.8725-2.14330.19221500.185823503X-RAY DIFFRACTION97
2.1433-2.69980.19941510.189423717X-RAY DIFFRACTION98
2.6998-24.7960.21410.190222140X-RAY DIFFRACTION91

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