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- PDB-9ojd: Crystal structure of E. coli diadenosine tetraphosphate hydrolase... -

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Basic information

Entry
Database: PDB / ID: 9ojd
TitleCrystal structure of E. coli diadenosine tetraphosphate hydrolase (ApaH)
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 7, 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)64,7187
Polymers64,3212
Non-polymers3975
Water9,458525
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2403
Polymers32,1611
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4784
Polymers32,1611
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.764, 55.224, 120.388
Angle α, β, γ (deg.)90.000, 129.570, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 80 or (resid 81...
d_2ens_1(chain "B" and (resid 2 through 78 or (resid 79...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLYGLYAA2 - 1902 - 190
d_12LEULEUARGARGAA192 - 270192 - 270
d_21ALAALAGLYGLYBB2 - 1902 - 190
d_22LEULEUARGARGBB192 - 270192 - 270

NCS oper: (Code: givenMatrix: (-0.0221127994763, -0.0512992880414, 0.998438484407), (0.0355187661153, -0.998092523697, -0.0504948650314), (0.999124337284, 0.0343467201832, 0.0238927072491)Vector: 3. ...NCS oper: (Code: given
Matrix: (-0.0221127994763, -0.0512992880414, 0.998438484407), (0.0355187661153, -0.998092523697, -0.0504948650314), (0.999124337284, 0.0343467201832, 0.0238927072491)
Vector: 3.5312931318, -27.8617875819, 5.02362263958)

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Components

#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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.43 Å3/Da / Density % sol: 64.14 %
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. Well solution: 0.1 M Bis-tris (pH 6.5), 0.3 M Sodium potassium tartrate, 18% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.77→28.56 Å / Num. obs: 82849 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5776 / CC1/2: 0.757 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
FAST_DPdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→28.56 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1983 2000 2.41 %
Rwork0.1826 80838 -
obs0.183 82838 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.91 Å2
Refinement stepCycle: LAST / Resolution: 1.77→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 19 525 4742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684343
X-RAY DIFFRACTIONf_angle_d0.94775924
X-RAY DIFFRACTIONf_chiral_restr0.0578637
X-RAY DIFFRACTIONf_plane_restr0.0106768
X-RAY DIFFRACTIONf_dihedral_angle_d15.1971595
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.481132292179 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.29441270.25485442X-RAY DIFFRACTION94.41
1.81-1.860.26951460.22875745X-RAY DIFFRACTION99.98
1.86-1.920.25411470.2145803X-RAY DIFFRACTION99.98
1.92-1.980.23621290.20885768X-RAY DIFFRACTION100
1.98-2.050.21421490.19555770X-RAY DIFFRACTION100
2.05-2.130.22241450.18745770X-RAY DIFFRACTION100
2.13-2.230.20631480.18485756X-RAY DIFFRACTION99.98
2.23-2.350.20071370.1865791X-RAY DIFFRACTION99.97
2.35-2.490.2191460.19395802X-RAY DIFFRACTION99.97
2.49-2.680.24641440.19685790X-RAY DIFFRACTION99.75
2.68-2.950.19661460.19775810X-RAY DIFFRACTION99.88
2.96-3.380.19491450.18765796X-RAY DIFFRACTION99.61
3.38-4.260.16441400.15685860X-RAY DIFFRACTION99.62
4.26-28.560.17611510.16715935X-RAY DIFFRACTION99.14

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