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- PDB-9ojw: Crystal structure of E. coli ApaH in complex with ADP, inactive state -

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Basic information

Entry
Database: PDB / ID: 9ojw
TitleCrystal structure of E. coli ApaH in complex with ADP, inactive state
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
ADENOSINE-5'-DIPHOSPHATE / : / Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 8, 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)65,72610
Polymers64,3212
Non-polymers1,4058
Water6,215345
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7905
Polymers32,1611
Non-polymers6294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9365
Polymers32,1611
Non-polymers7754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)166.583, 54.674, 119.269
Angle α, β, γ (deg.)90.00, 129.32, 90.00
Int Tables number5
Space group name H-MC121

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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, 353 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#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.: 345 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 25 mM Hepes (pH 7.5), 0.2 M NaCl. Well solution: 0.1 M Ammonium citrate, 17% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.3625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3625 Å / Relative weight: 1
ReflectionResolution: 1.94→92.27 Å / Num. obs: 60792 / % possible obs: 97.9 % / Redundancy: 4.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.128 / Net I/σ(I): 6.8
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 4 % / Rmerge(I) obs: 1.196 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3797 / CC1/2: 0.357 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→92.27 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 3795 3.41 %
Rwork0.193 --
obs0.194 60792 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→92.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 79 345 4642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094507
X-RAY DIFFRACTIONf_angle_d1.0646162
X-RAY DIFFRACTIONf_dihedral_angle_d6.643626
X-RAY DIFFRACTIONf_chiral_restr0.066655
X-RAY DIFFRACTIONf_plane_restr0.009789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.980.36031290.31673807X-RAY DIFFRACTION91
1.98-2.010.31051360.30864037X-RAY DIFFRACTION95
2.01-2.040.32871670.28893963X-RAY DIFFRACTION96
2.04-2.070.27711550.2924011X-RAY DIFFRACTION96
2.07-2.10.28441350.29274135X-RAY DIFFRACTION97
2.1-2.130.26691430.27223954X-RAY DIFFRACTION96
2.13-2.170.30311300.2753963X-RAY DIFFRACTION95
2.17-2.20.30471320.2773925X-RAY DIFFRACTION94
2.2-2.240.27291500.26144065X-RAY DIFFRACTION96
2.24-2.290.30241600.25894045X-RAY DIFFRACTION97
2.29-2.330.27471460.23974005X-RAY DIFFRACTION98
2.33-2.380.25081460.23534164X-RAY DIFFRACTION98
2.38-2.440.27231250.22964019X-RAY DIFFRACTION98
2.44-2.50.26981310.22234151X-RAY DIFFRACTION98
2.5-2.570.27421390.21984043X-RAY DIFFRACTION97
2.57-2.640.24191610.22794087X-RAY DIFFRACTION97
2.64-2.730.2371440.21634069X-RAY DIFFRACTION97
2.73-2.830.22011320.21074046X-RAY DIFFRACTION97
2.83-2.940.26151400.20433970X-RAY DIFFRACTION96
2.94-3.070.2221340.19873795X-RAY DIFFRACTION90
3.07-3.240.25451480.18713996X-RAY DIFFRACTION95
3.24-3.440.20781420.18133997X-RAY DIFFRACTION95
3.44-3.70.18671270.15923845X-RAY DIFFRACTION93
3.7-4.080.15931290.14123793X-RAY DIFFRACTION91
4.08-4.670.16771420.13083807X-RAY DIFFRACTION91
4.67-5.880.1411280.14213753X-RAY DIFFRACTION89
5.88-92.270.15921440.1523955X-RAY DIFFRACTION95

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