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- PDB-9on7: Crystal structure of E. coli ApaH in complex with ppAG -

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Basic information

Entry
Database: PDB / ID: 9on7
TitleCrystal structure of E. coli ApaH in complex with ppAG
Components
  • Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
  • RNA ppAG
KeywordsHYDROLASE / ApaH / symmetrical hydrolase / RNA decapping
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / RNA decapping / nucleobase-containing small molecule interconversion / phosphatase activity / response to X-ray / hydrolase activity / cytoplasm
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase, symmetrical / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / RNA / Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsNuthanakanti, A. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112940 United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: ApaH decaps Np 4 N-capped RNAs in two alternative orientations.
Authors: Nuthanakanti, A. / Korn, M. / Levenson-Palmer, R. / Wu, Y. / Babu, N.R. / Huang, X. / Banh, R.S. / Belasco, J.G. / Serganov, A.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
C: RNA ppAG
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
D: RNA ppAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,91918
Polymers65,7404
Non-polymers1,17914
Water10,377576
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
C: RNA ppAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2928
Polymers32,8702
Non-polymers4226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
D: RNA ppAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,62710
Polymers32,8702
Non-polymers7578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.882, 55.498, 121.205
Angle α, β, γ (deg.)90.00, 129.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein Bis(5'-nucleosyl)-tetraphosphatase [symmetrical] / Ap4A hydrolase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate pyrophosphohydrolase / Diadenosine ...Ap4A hydrolase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate pyrophosphohydrolase / Diadenosine tetraphosphatase


Mass: 32160.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: apaH, b0049, JW0048 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P05637, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
#2: RNA chain RNA ppAG


Mass: 709.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 590 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.52 Å3/Da / Density % sol: 65.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 2 mM ppAG, 3 mM MgCl2, 10 mM Ca(OAc)2, 25 mM Hepes (pH 7.5), 0.2 M NaCl. Well solution: 0.1 M Hepes (pH 7.5), 1.0 M Ammonium sulfate, 0.5% PEG8K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.79→28.73 Å / Num. obs: 78435 / % possible obs: 97.1 % / Redundancy: 5.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.5
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2 / Num. unique obs: 5385 / CC1/2: 0.724 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
FAST_DPdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→28.73 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 1980 2.52 %
Rwork0.212 --
obs0.213 78416 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 62 56 576 4891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084509
X-RAY DIFFRACTIONf_angle_d1.0056176
X-RAY DIFFRACTIONf_dihedral_angle_d12.841626
X-RAY DIFFRACTIONf_chiral_restr0.061655
X-RAY DIFFRACTIONf_plane_restr0.007782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.31221310.27695039X-RAY DIFFRACTION90
1.84-1.890.29491380.24475380X-RAY DIFFRACTION96
1.89-1.940.29171350.24035424X-RAY DIFFRACTION96
1.94-2.010.26691480.23385386X-RAY DIFFRACTION97
2.01-2.080.27461380.22195434X-RAY DIFFRACTION97
2.08-2.160.29421420.21985448X-RAY DIFFRACTION97
2.16-2.260.24411480.22145416X-RAY DIFFRACTION97
2.26-2.380.25541370.21355489X-RAY DIFFRACTION97
2.38-2.530.25791460.21655481X-RAY DIFFRACTION97
2.53-2.720.25491340.21735486X-RAY DIFFRACTION98
2.72-30.26191470.22015516X-RAY DIFFRACTION98
3-3.430.25381430.21595593X-RAY DIFFRACTION98
3.43-4.320.21381460.17985603X-RAY DIFFRACTION98
4.32-28.730.20411470.20425741X-RAY DIFFRACTION99

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