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- PDB-8j6h: Structure and allosteric regulation of the inosine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 8j6h
TitleStructure and allosteric regulation of the inosine 5'-monophosphate-specific phosphatase ISN1 from Saccharomyces cerevisiae
ComponentsIMP-specific 5'-nucleotidase 1
KeywordsHYDROLASE / hydrolysis / phosphatase
Function / homology
Function and homology information


nicotinamide riboside biosynthetic process / nicotinic acid riboside biosynthetic process / inosine salvage / IMP-specific 5'-nucleotidase / : / nucleotide metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
IMP-specific 5-nucleotidase / IMP-specific 5'-nucleotidase / HAD-like superfamily
Similarity search - Domain/homology
INOSINE / IMP-specific 5'-nucleotidase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44074489024 Å
AuthorsByun, S.J. / Rhee, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C2092118 Korea, Republic Of
Ministry of Science, ICT and Future Planning (MSIP)RS-2023-00207820 Korea, Republic Of
CitationJournal: Febs J. / Year: 2024
Title: Structure, cooperativity and inhibition of the inosine 5'-monophosphate-specific phosphatase from Saccharomyces cerevisiae.
Authors: Byun, S. / Park, C. / Suh, J.Y. / Witte, C.P. / Rhee, S.
History
DepositionApr 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMP-specific 5'-nucleotidase 1
B: IMP-specific 5'-nucleotidase 1
C: IMP-specific 5'-nucleotidase 1
D: IMP-specific 5'-nucleotidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,5908
Polymers209,5174
Non-polymers1,0734
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint-44 kcal/mol
Surface area65150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.391, 165.061, 82.672
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
IMP-specific 5'-nucleotidase 1


Mass: 52379.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ISN1, YOR155C, O3548 / Variant: DELTA4R / Plasmid: pET41a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli / References: UniProt: Q99312, IMP-specific 5'-nucleotidase
#2: Chemical
ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.26M ammonium dihydrogen phosphate, 35% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 74898 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 55.7092581885 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.34
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 5.5 % / Num. unique obs: 7175 / CC1/2: 0.48 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.44074489024→47.0886773127 Å / SU ML: 0.40257673769 / Cross valid method: FREE R-VALUE / σ(F): 0.239701093081 / Phase error: 32.3227285541
RfactorNum. reflection% reflection
Rfree0.278814374216 2000 2.67444037335 %
Rwork0.235677868256 72782 -
obs0.236825102162 74782 98.7847084621 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.3725873448 Å2
Refinement stepCycle: LAST / Resolution: 2.44074489024→47.0886773127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13029 0 76 44 13149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032699581443713378
X-RAY DIFFRACTIONf_angle_d0.73093648620718100
X-RAY DIFFRACTIONf_chiral_restr0.02709784739192000
X-RAY DIFFRACTIONf_plane_restr0.004279286869292343
X-RAY DIFFRACTIONf_dihedral_angle_d15.37538377454966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.441-2.50180.4022823860831250.3631006255344528X-RAY DIFFRACTION86.9069854315
2.5018-2.56940.398825266071390.3492619157185079X-RAY DIFFRACTION98.1380477713
2.5694-2.6450.3622089029781410.3208402285785131X-RAY DIFFRACTION99.2096349266
2.645-2.73040.3767858083411430.2958240198035206X-RAY DIFFRACTION99.7389520791
2.7304-2.8280.3395116861021430.2917262624675212X-RAY DIFFRACTION99.9813293503
2.828-2.94120.3367236460711440.2857616195485222X-RAY DIFFRACTION99.9627421759
2.9412-3.0750.3962465392831430.2673265372835232X-RAY DIFFRACTION99.7032090521
3.075-3.23710.3030019885091440.2518803192395195X-RAY DIFFRACTION99.8877455566
3.2371-3.43980.2766237905751430.2346864632025247X-RAY DIFFRACTION99.9629080119
3.4398-3.70530.2450498177911440.2259248778825232X-RAY DIFFRACTION99.8699609883
3.7053-4.0780.2717208991511460.2168240569475281X-RAY DIFFRACTION99.9815770081
4.078-4.66770.2337242102071450.1960112960765300X-RAY DIFFRACTION99.9449339207
4.6677-5.8790.2436074810951470.2257661217435366X-RAY DIFFRACTION99.891284653
5.879-470.2514770359931530.2111656424765551X-RAY DIFFRACTION99.6680062904

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