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- PDB-9oqb: Crystal structure of E. coli ApaH in complex with Up4AGG -

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Basic information

Entry
Database: PDB / ID: 9oqb
TitleCrystal structure of E. coli ApaH in complex with Up4AGG
Components
  • Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
  • RNA Up4AGG
KeywordsHYDROLASE / ApaH / symmetrical hydrolase / RNA decapping
Function / homologyBis(5'-nucleosyl)-tetraphosphatase, symmetrical / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / : / RNA / Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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

Downloads & links

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Assembly

Deposited unit
A: Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
B: Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
C: RNA Up4AGG
D: RNA Up4AGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,99414
Polymers67,2034
Non-polymers79110
Water4,846269
1
A: Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
C: RNA Up4AGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9247
Polymers33,6012
Non-polymers3225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
D: RNA Up4AGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0707
Polymers33,6012
Non-polymers4695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.177, 55.030, 120.179
Angle α, β, γ (deg.)90.00, 129.77, 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, BWG_0047 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C4ZPX5, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
#2: RNA chain RNA Up4AGG


Mass: 1440.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 279 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.49 Å3/Da / Density % sol: 64.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 4 mM MgCl2, 10 mM Ca(OAc)2, 25 mM Hepes (pH 7.5), 0.1 M NaCl and soaked with Up4AGG. 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: 0.97903 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: 2.03→29 Å / Num. obs: 52609 / % possible obs: 97.6 % / Redundancy: 4.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.145 / Net I/σ(I): 29.6
Reflection shellResolution: 2.03→2.06 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.184 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2508 / CC1/2: 0.401 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→28.45 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 3803 3.79 %
Rwork0.2012 --
obs0.2019 52609 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 100 269 4571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054437
X-RAY DIFFRACTIONf_angle_d0.9626069
X-RAY DIFFRACTIONf_dihedral_angle_d15.762628
X-RAY DIFFRACTIONf_chiral_restr0.055648
X-RAY DIFFRACTIONf_plane_restr0.006770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.060.40231030.3732813X-RAY DIFFRACTION75
2.06-2.090.36081440.33693432X-RAY DIFFRACTION93
2.09-2.120.32041400.3183554X-RAY DIFFRACTION93
2.12-2.150.26611450.29933605X-RAY DIFFRACTION95
2.15-2.180.29971150.27853586X-RAY DIFFRACTION95
2.18-2.210.29391670.27793512X-RAY DIFFRACTION95
2.21-2.250.31841520.27083547X-RAY DIFFRACTION95
2.25-2.290.29941490.26783583X-RAY DIFFRACTION95
2.29-2.330.30971210.26683600X-RAY DIFFRACTION95
2.33-2.370.27741470.25073583X-RAY DIFFRACTION95
2.37-2.420.29211240.24133589X-RAY DIFFRACTION95
2.42-2.480.24041380.22673648X-RAY DIFFRACTION95
2.48-2.530.26111560.22163543X-RAY DIFFRACTION95
2.53-2.60.19911190.22963602X-RAY DIFFRACTION95
2.6-2.670.25881310.22323563X-RAY DIFFRACTION95
2.67-2.740.23451610.22033636X-RAY DIFFRACTION96
2.75-2.830.24861300.20273654X-RAY DIFFRACTION97
2.83-2.930.22831610.19853718X-RAY DIFFRACTION98
2.93-3.050.20291470.18553610X-RAY DIFFRACTION98
3.05-3.190.1971450.1873690X-RAY DIFFRACTION98
3.19-3.360.18261410.17663670X-RAY DIFFRACTION98
3.36-3.570.18471300.17623681X-RAY DIFFRACTION97
3.57-3.840.17121460.1543638X-RAY DIFFRACTION97
3.84-4.230.17761540.15133631X-RAY DIFFRACTION96
4.23-4.840.16861440.14893557X-RAY DIFFRACTION95
4.84-6.090.20771500.19263609X-RAY DIFFRACTION96
6.09-28.450.23371430.19593685X-RAY DIFFRACTION98

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