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- PDB-9m7l: Crystal structure of Pseudouridine 5'-monophosphate phosphatase f... -

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Basic information

Entry
Database: PDB / ID: 9m7l
TitleCrystal structure of Pseudouridine 5'-monophosphate phosphatase from human (hHDHD1A) in the unliganded state
ComponentsPseudouridine-5'-phosphatase
KeywordsRNA BINDING PROTEIN / pseudouridine monophosphate phosphatase / HAD phosphatase / cofactor
Function / homology
Function and homology information


pseudouridine 5'-phosphatase / pseudouridine 5'-phosphatase activity / Pyrimidine salvage / nucleotide metabolic process / phosphatase activity / metal ion binding / cytosol
Similarity search - Function
Phosphatase Gpp1/Gpp2-like / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Pseudouridine-5'-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsSeo, S. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural and functional insights in the substrate specificity of the pseudouridine monophosphate phosphatase HDHD1A.
Authors: Seo, S. / Kim, M. / Rhee, S.
History
DepositionMar 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudouridine-5'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0992
Polymers25,0751
Non-polymers241
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.560, 60.960, 68.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

21A-664-

HOH

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Components

#1: Protein Pseudouridine-5'-phosphatase / Haloacid dehalogenase-like hydrolase domain-containing protein 1 / Haloacid dehalogenase-like ...Haloacid dehalogenase-like hydrolase domain-containing protein 1 / Haloacid dehalogenase-like hydrolase domain-containing protein 1A / Protein GS1 / Pseudouridine-5'-monophosphatase / 5'-PsiMPase


Mass: 25074.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUDP, DXF68S1E, FAM16AX, GS1, HDHD1, HDHD1A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08623, pseudouridine 5'-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl (pH 8.5), 30% (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: 0.97933 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.36→30 Å / Num. obs: 88114 / % possible obs: 99 % / Redundancy: 12.9 % / CC1/2: 0.99 / Net I/σ(I): 29.36
Reflection shellResolution: 1.36→1.41 Å / Num. unique obs: 4568 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSv20230630data reduction
XDSv20230630data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 1.36→28.384 Å / SU ML: 0.08 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 14.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1575 3826 4.34 %
Rwork0.1486 --
obs0.149 88113 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→28.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 1 308 2060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071792
X-RAY DIFFRACTIONf_angle_d1.1482430
X-RAY DIFFRACTIONf_dihedral_angle_d12.491671
X-RAY DIFFRACTIONf_chiral_restr0.061277
X-RAY DIFFRACTIONf_plane_restr0.006314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.37720.17651390.18353033X-RAY DIFFRACTION97
1.3772-1.39530.23781380.18063063X-RAY DIFFRACTION97
1.3953-1.41450.21831380.17763073X-RAY DIFFRACTION98
1.4145-1.43470.19841360.16933085X-RAY DIFFRACTION97
1.4347-1.45610.19281430.16823123X-RAY DIFFRACTION99
1.4561-1.47880.20681380.17143107X-RAY DIFFRACTION98
1.4788-1.50310.19671380.16193074X-RAY DIFFRACTION99
1.5031-1.5290.17931420.16283093X-RAY DIFFRACTION98
1.529-1.55680.14991390.15583145X-RAY DIFFRACTION98
1.5568-1.58670.17521410.14613117X-RAY DIFFRACTION99
1.5867-1.61910.19241400.15233129X-RAY DIFFRACTION99
1.6191-1.65430.13621400.1573130X-RAY DIFFRACTION100
1.6543-1.69280.13681430.15553150X-RAY DIFFRACTION99
1.6928-1.73510.16291410.15283102X-RAY DIFFRACTION99
1.7351-1.7820.17091420.14853093X-RAY DIFFRACTION99
1.782-1.83450.15041440.14853191X-RAY DIFFRACTION100
1.8345-1.89370.14551390.14593110X-RAY DIFFRACTION100
1.8937-1.96130.17451480.13993145X-RAY DIFFRACTION100
1.9613-2.03980.14171450.13473159X-RAY DIFFRACTION100
2.0398-2.13260.15891430.13893135X-RAY DIFFRACTION100
2.1326-2.2450.12591470.13543147X-RAY DIFFRACTION100
2.245-2.38560.15471400.14153133X-RAY DIFFRACTION100
2.3856-2.56970.16741440.13693171X-RAY DIFFRACTION100
2.5697-2.82810.15181410.15483139X-RAY DIFFRACTION100
2.8281-3.23680.16851480.16063157X-RAY DIFFRACTION100
3.2368-4.07610.16661420.13683142X-RAY DIFFRACTION100
4.0761-28.3840.13291470.15413141X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 75.106 Å / Origin y: 77.0546 Å / Origin z: 79.7215 Å
111213212223313233
T0.0589 Å2-0.0079 Å2-0.0118 Å2-0.0411 Å20.0051 Å2--0.0584 Å2
L0.7869 °20.0273 °2-0.0564 °2-0.7628 °20.0808 °2--1.0785 °2
S0.0029 Å °-0.0192 Å °-0.0068 Å °0.0814 Å °-0.031 Å °-0.0343 Å °0.04 Å °0.0177 Å °-0.0022 Å °
Refinement TLS groupSelection details: all

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