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- PDB-9omx: Crystal structure of E. coli ApaH in complex with Up4U -

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Basic information

Entry
Database: PDB / ID: 9omx
TitleCrystal structure of E. coli ApaH in complex with Up4U
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: 1.54 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)66,88916
Polymers64,3212
Non-polymers2,56814
Water13,655758
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3738
Polymers32,1611
Non-polymers1,2137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5158
Polymers32,1611
Non-polymers1,3557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.727, 54.964, 120.435
Angle α, β, γ (deg.)90.00, 129.93, 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 , 6 types, 772 molecules

#2: Chemical ChemComp-A1CC9 / [[(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] [[[(3~{S},4~{S},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


Mass: 790.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26N4O23P4 / 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: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / 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.: 758 / 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: 3.5 Å3/Da / Density % sol: 64.87 %
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), 0.2 M NaCl and soaked with Up4U. 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: 0.97932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.54→29 Å / Num. obs: 121656 / % possible obs: 99 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.122 / Net I/σ(I): 19.2
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6013 / CC1/2: 0.519 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→28.37 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 3743 1.65 %
Rwork0.1773 --
obs0.1776 121656 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4210 0 112 758 5080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094509
X-RAY DIFFRACTIONf_angle_d1.0566172
X-RAY DIFFRACTIONf_dihedral_angle_d8.336625
X-RAY DIFFRACTIONf_chiral_restr0.071653
X-RAY DIFFRACTIONf_plane_restr0.009783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.40181190.35737179X-RAY DIFFRACTION81
1.56-1.580.37091250.33257787X-RAY DIFFRACTION89
1.58-1.60.30491370.31117964X-RAY DIFFRACTION91
1.6-1.630.32821260.28258092X-RAY DIFFRACTION92
1.63-1.650.24251590.26778127X-RAY DIFFRACTION93
1.65-1.680.26611110.25088117X-RAY DIFFRACTION93
1.68-1.710.32681400.24768218X-RAY DIFFRACTION93
1.71-1.730.26871570.24088166X-RAY DIFFRACTION94
1.73-1.770.26141180.22968376X-RAY DIFFRACTION94
1.77-1.80.2291480.2258328X-RAY DIFFRACTION95
1.8-1.840.23121370.22478280X-RAY DIFFRACTION94
1.84-1.880.23441350.2098371X-RAY DIFFRACTION96
1.88-1.920.20211680.18578521X-RAY DIFFRACTION97
1.92-1.970.21861370.18248561X-RAY DIFFRACTION98
1.97-2.020.19051400.18018547X-RAY DIFFRACTION97
2.02-2.080.16881250.17328514X-RAY DIFFRACTION97
2.08-2.150.20031760.16858542X-RAY DIFFRACTION97
2.15-2.230.20931240.1678502X-RAY DIFFRACTION97
2.23-2.310.17561370.16618472X-RAY DIFFRACTION97
2.31-2.420.18541410.1698435X-RAY DIFFRACTION96
2.42-2.550.18621450.16038533X-RAY DIFFRACTION97
2.55-2.710.1741550.17238363X-RAY DIFFRACTION96
2.71-2.920.18861280.16338583X-RAY DIFFRACTION97
2.92-3.210.19031430.16168454X-RAY DIFFRACTION96
3.21-3.670.18311470.1458389X-RAY DIFFRACTION95
3.67-4.620.13841240.13847806X-RAY DIFFRACTION89
4.62-28.370.16661410.1668045X-RAY DIFFRACTION92

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