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- PDB-9oq9: Crystal structure of E. coli ApaH in complex with Ap4AGG -

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Basic information

Entry
Database: PDB / ID: 9oq9
TitleCrystal structure of E. coli ApaH in complex with Ap4AGG
ComponentsBis(5'-nucleosyl)-tetraphosphatase [symmetrical]
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
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / : / Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,50111
Polymers64,3212
Non-polymers2,1799
Water7,314406
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1315
Polymers32,1611
Non-polymers9714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3696
Polymers32,1611
Non-polymers1,2095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.633, 55.019, 120.040
Angle α, β, γ (deg.)90.000, 129.800, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 415 molecules

#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O19P4 / Details: The full molecule is RNA Ap4AGG / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 4 mM MgCl2, 10 mM Ca(OAc)2, 1 mM DTT, 25 mM Hepes (pH 7.5), 0.1 M NaCl and soaked with Ap4AGG. Well solution: 0.1 M Hepes (pH 7.5), 0.2 M Li2SO4, 25% PEG3350.

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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: 0.97903 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.96→29.51 Å / Num. obs: 59755 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 25.17 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.124 / Net I/σ(I): 7.9
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4152 / CC1/2: 0.706 / % possible all: 94.5

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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: 1.96→29.51 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 1997 3.34 %
Rwork0.2074 57745 -
obs0.2084 59742 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.55 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 91 406 4701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814413
X-RAY DIFFRACTIONf_angle_d0.98926034
X-RAY DIFFRACTIONf_chiral_restr0.057643
X-RAY DIFFRACTIONf_plane_restr0.0076769
X-RAY DIFFRACTIONf_dihedral_angle_d18.5942637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.33861260.27543878X-RAY DIFFRACTION94.15
2.01-2.070.27631490.24524091X-RAY DIFFRACTION99.74
2.07-2.130.26191480.22364112X-RAY DIFFRACTION99.74
2.13-2.190.27511390.21544142X-RAY DIFFRACTION99.86
2.19-2.270.25171280.21184082X-RAY DIFFRACTION99.83
2.27-2.360.2551570.20494140X-RAY DIFFRACTION99.93
2.36-2.470.23251400.20364125X-RAY DIFFRACTION99.72
2.47-2.60.25511390.21044142X-RAY DIFFRACTION99.81
2.6-2.770.23361500.2124124X-RAY DIFFRACTION99.74
2.77-2.980.26831410.21554122X-RAY DIFFRACTION99.84
2.98-3.280.24921470.2134162X-RAY DIFFRACTION99.75
3.28-3.750.21271450.20134153X-RAY DIFFRACTION99.61
3.75-4.720.20781400.18094187X-RAY DIFFRACTION99.7
4.72-29.510.21081480.20624285X-RAY DIFFRACTION99.46

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