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- PDB-9on0: Crystal structure of E. coli ApaH D37A mutant in complex with Ap4U -

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Basic information

Entry
Database: PDB / ID: 9on0
TitleCrystal structure of E. coli ApaH D37A mutant in complex with Ap4U
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(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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

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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)66,2087
Polymers64,2332
Non-polymers1,9755
Water10,178565
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9853
Polymers32,1171
Non-polymers8682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2234
Polymers32,1171
Non-polymers1,1073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.055, 55.033, 119.751
Angle α, β, γ (deg.)90.00, 129.58, 90.00
Int Tables number5
Space group name H-MC121
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

#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: 32116.523 Da / Num. of mol.: 2 / Mutation: D37A
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: Chemical ChemComp-A1L89 / P1-(5'-Adenosyl) P4-(5'-uridyl) tetraphosphate / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate / Adenosine(5')tetraphosphate uridine / Ap4U


Mass: 813.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N7O21P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (D37A) mutant (10 mg/mL), 1 mM DTT, 25 mM Hepes (pH 7.5), 0.2 M NaCl and soaked with Ap4U. Well solution: 0.2 M Trisodium Citrate, 20% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.82→32.2 Å / Num. obs: 74138 / % possible obs: 99.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 25.15 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.184 / Net I/σ(I): 5.2
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.735 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3633 / CC1/2: 0.355 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata scaling
autoPROCdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→32.2 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 3693 5 %
Rwork0.1908 --
obs0.1923 73812 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→32.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 0 71 565 4835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084412
X-RAY DIFFRACTIONf_angle_d1.0526032
X-RAY DIFFRACTIONf_dihedral_angle_d8.539623
X-RAY DIFFRACTIONf_chiral_restr0.056641
X-RAY DIFFRACTIONf_plane_restr0.007767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.36911440.3522490X-RAY DIFFRACTION95
1.85-1.880.33961530.30482605X-RAY DIFFRACTION98
1.88-1.910.35331360.29132715X-RAY DIFFRACTION98
1.91-1.930.27991240.27742641X-RAY DIFFRACTION99
1.93-1.960.31151390.26532743X-RAY DIFFRACTION99
1.96-20.32231660.25692623X-RAY DIFFRACTION99
2-2.030.28011510.25252681X-RAY DIFFRACTION100
2.03-2.070.29171430.23052662X-RAY DIFFRACTION100
2.07-2.110.26341320.22792720X-RAY DIFFRACTION100
2.11-2.150.21651370.21932717X-RAY DIFFRACTION100
2.15-2.20.27071400.21222743X-RAY DIFFRACTION100
2.2-2.250.30321160.21362657X-RAY DIFFRACTION100
2.25-2.30.25291300.21642744X-RAY DIFFRACTION100
2.3-2.370.25291430.20822686X-RAY DIFFRACTION100
2.37-2.440.26431350.19572713X-RAY DIFFRACTION100
2.44-2.520.21031610.19372690X-RAY DIFFRACTION100
2.52-2.60.23391480.19052699X-RAY DIFFRACTION100
2.61-2.710.2261620.192665X-RAY DIFFRACTION100
2.71-2.830.21121410.192713X-RAY DIFFRACTION100
2.83-2.980.23241410.19092715X-RAY DIFFRACTION100
2.98-3.170.23391320.19772729X-RAY DIFFRACTION100
3.17-3.410.2371340.1792733X-RAY DIFFRACTION100
3.41-3.760.17191260.15952744X-RAY DIFFRACTION99
3.76-4.30.17111450.1422718X-RAY DIFFRACTION99
4.3-5.410.151380.14852763X-RAY DIFFRACTION100
5.41-32.20.18451760.17222810X-RAY DIFFRACTION100

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