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- PDB-9om9: Crystal structure of E. coli ApaH in complex with AppCH2ppA -

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Basic information

Entry
Database: PDB / ID: 9om9
TitleCrystal structure of E. coli ApaH in complex with AppCH2ppA
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: 1.77 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 13, 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,49711
Polymers64,3212
Non-polymers2,1759
Water11,007611
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1295
Polymers32,1611
Non-polymers9694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3676
Polymers32,1611
Non-polymers1,2075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.525, 54.958, 119.606
Angle α, β, γ (deg.)90.00, 129.50, 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

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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, 620 molecules

#2: Chemical ChemComp-A1CCP / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[[[(3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphinic acid


Mass: 834.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N10O18P4 / Feature type: SUBJECT OF INVESTIGATION
#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: 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: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 64.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 10 mM MgCl2, 25 mM Hepes (pH 7.5), 0.2 M NaCl and soaked with AppCH2ppA. Well solution: 0.1 M Bis-tris (pH 6.5), 0.2 M Sodium potassium tartrate, 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-2 / Wavelength: 0.91886 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91886 Å / Relative weight: 1
ReflectionResolution: 1.77→28.37 Å / Num. obs: 80755 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.86 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2 / Num. unique obs: 5471 / CC1/2: 0.736 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
FAST_DPdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→28.37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 1996 2.47 %
Rwork0.1734 --
obs0.1739 80745 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 91 611 4920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074487
X-RAY DIFFRACTIONf_angle_d1.0456139
X-RAY DIFFRACTIONf_dihedral_angle_d8.863643
X-RAY DIFFRACTIONf_chiral_restr0.064651
X-RAY DIFFRACTIONf_plane_restr0.007783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.28431280.24955115X-RAY DIFFRACTION91
1.82-1.870.25941360.22215645X-RAY DIFFRACTION100
1.87-1.920.22461410.20545608X-RAY DIFFRACTION100
1.92-1.980.2321530.20485631X-RAY DIFFRACTION100
1.98-2.050.21791410.19225658X-RAY DIFFRACTION100
2.05-2.140.20221520.17785632X-RAY DIFFRACTION100
2.14-2.230.20451320.17685612X-RAY DIFFRACTION100
2.23-2.350.21531470.17725639X-RAY DIFFRACTION100
2.35-2.50.19981440.1815673X-RAY DIFFRACTION100
2.5-2.690.23291360.18235649X-RAY DIFFRACTION100
2.69-2.960.20291460.18565648X-RAY DIFFRACTION100
2.96-3.390.18071430.1775694X-RAY DIFFRACTION100
3.39-4.270.15651440.14595712X-RAY DIFFRACTION100
4.27-28.370.17261530.15645833X-RAY DIFFRACTION100

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