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- PDB-9oph: Crystal structure of E. coli ApaH in complex with Up4AG -

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Basic information

Entry
Database: PDB / ID: 9oph
TitleCrystal structure of E. coli ApaH in complex with Up4AG
Components
  • Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
  • RNA Up4AG
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
: / RNA / Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 19, 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]
C: RNA Up4AG
D: RNA Up4AG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,30714
Polymers66,5124
Non-polymers79510
Water9,656536
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
C: RNA Up4AG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4866
Polymers33,2562
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
D: RNA Up4AG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8218
Polymers33,2562
Non-polymers5656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.975, 54.909, 120.027
Angle α, β, γ (deg.)90.00, 129.73, 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 / 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, b0049, JW0048 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P05637, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
#2: RNA chain RNA Up4AG


Mass: 1095.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 546 molecules

#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.: 3 / 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.: 536 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
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 Up4AG. 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: 0.97942 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.66→30 Å / Num. obs: 99184 / % possible obs: 99 % / Redundancy: 5.3 % / Biso Wilson estimate: 18.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.6
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4817 / CC1/2: 0.596 / % possible all: 97.7

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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: 1.66→29.85 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 3815 2.01 %
Rwork0.1743 --
obs0.1747 99184 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 114 536 4851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144435
X-RAY DIFFRACTIONf_angle_d1.2816066
X-RAY DIFFRACTIONf_dihedral_angle_d15.088624
X-RAY DIFFRACTIONf_chiral_restr0.088646
X-RAY DIFFRACTIONf_plane_restr0.009771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.670.26111170.30375339X-RAY DIFFRACTION74
1.67-1.690.34951280.29526638X-RAY DIFFRACTION92
1.69-1.720.28591260.28616696X-RAY DIFFRACTION94
1.72-1.740.24961240.28396742X-RAY DIFFRACTION95
1.74-1.770.2651660.27236904X-RAY DIFFRACTION96
1.77-1.790.23871520.2456926X-RAY DIFFRACTION96
1.79-1.820.26141360.22716953X-RAY DIFFRACTION97
1.82-1.860.23941330.21346883X-RAY DIFFRACTION97
1.86-1.890.22351500.20187008X-RAY DIFFRACTION97
1.89-1.930.24931370.19666935X-RAY DIFFRACTION98
1.93-1.960.26061390.19557034X-RAY DIFFRACTION98
1.96-2.010.22251500.19196896X-RAY DIFFRACTION98
2.01-2.050.2221400.19167032X-RAY DIFFRACTION98
2.05-2.110.17271320.17277000X-RAY DIFFRACTION98
2.11-2.160.21971690.16796938X-RAY DIFFRACTION98
2.16-2.230.19741230.16487015X-RAY DIFFRACTION98
2.23-2.30.20311470.1657091X-RAY DIFFRACTION98
2.3-2.380.18221440.16337028X-RAY DIFFRACTION99
2.38-2.480.17491480.15837004X-RAY DIFFRACTION98
2.48-2.590.18181430.16557103X-RAY DIFFRACTION99
2.59-2.720.16671530.16397024X-RAY DIFFRACTION99
2.72-2.890.21181500.16567098X-RAY DIFFRACTION99
2.89-3.120.14761410.15897075X-RAY DIFFRACTION99
3.12-3.430.19231440.167088X-RAY DIFFRACTION99
3.43-3.930.17441370.14316822X-RAY DIFFRACTION96
3.93-4.940.15671460.1426971X-RAY DIFFRACTION97
4.94-29.850.19031400.17637026X-RAY DIFFRACTION98

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