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- PDB-8jb3: Structure and allosteric regulation of the inosine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 8jb3
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
INOSINIC ACID / INOSINE / PHOSPHATE ION / IMP-specific 5'-nucleotidase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77382458733 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
DepositionMay 8, 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 1.2Nov 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,0956
Polymers52,3351
Non-polymers7605
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.591, 180.591, 90.98
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 52335.164 Da / Num. of mol.: 1 / Mutation: D172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BL21(DE3) / Gene: ISN1, YOR155C, O3548 / Variant: DELTA4R / Plasmid: pET41a / Cell line (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DELTA4R / References: UniProt: Q99312, IMP-specific 5'-nucleotidase

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.7 M ammonium dihydrogen phosphate, 0.07 M sodium citrate (pH 5.6), 30% glycerol

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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: 0.97954 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 72288 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 33.3265142755 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.3
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 7534 / CC1/2: 0.38

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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: 1.77382458733→31.4654581115 Å / SU ML: 0.264342707946 / Cross valid method: FREE R-VALUE / σ(F): 1.32593671838 / Phase error: 31.0746381815
RfactorNum. reflection% reflection
Rfree0.23735416093 1959 2.75670883582 %
Rwork0.211272875738 69104 -
obs0.211991224589 71063 98.2021447128 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.3334018587 Å2
Refinement stepCycle: LAST / Resolution: 1.77382458733→31.4654581115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 49 189 3609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214221674253490
X-RAY DIFFRACTIONf_angle_d1.314385305064732
X-RAY DIFFRACTIONf_chiral_restr0.0598048233248522
X-RAY DIFFRACTIONf_plane_restr0.00594968061866611
X-RAY DIFFRACTIONf_dihedral_angle_d13.42133079621287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.81820.3691851596021290.3883295063924643X-RAY DIFFRACTION93.385518591
1.8182-1.86730.3457314115471380.3762572813274800X-RAY DIFFRACTION96.7666078777
1.8673-1.92230.3584418814641400.3664917507414922X-RAY DIFFRACTION99.2549019608
1.9223-1.98430.3645574496091420.3297503209744984X-RAY DIFFRACTION99.883086516
1.9843-2.05520.3049218624031420.2904469328424980X-RAY DIFFRACTION99.9609679938
2.0552-2.13750.2907181110131410.2591020855764957X-RAY DIFFRACTION99.8433215825
2.1375-2.23470.2749578555431420.2408361266064973X-RAY DIFFRACTION99.8243559719
2.2347-2.35250.2820899818641420.2279137716924989X-RAY DIFFRACTION99.4765412951
2.3525-2.49990.298117029661380.2339100909754945X-RAY DIFFRACTION98.6990291262
2.4999-2.69280.2538306630591370.2283834794944910X-RAY DIFFRACTION97.7343144849
2.6928-2.96360.2826646017691390.2239894551874891X-RAY DIFFRACTION97.1229967175
2.9636-3.3920.2194988726691410.2042230979414898X-RAY DIFFRACTION96.773574035
3.392-4.27190.2099853873281410.1688712696534996X-RAY DIFFRACTION97.6987447699
4.2719-31.460.1737532087811470.170797392595216X-RAY DIFFRACTION98.4578667156

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