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- PDB-9oly: Crystal structure of E. coli ApaH D37A mutant, apo form -

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Basic information

Entry
Database: PDB / ID: 9oly
TitleCrystal structure of E. coli ApaH D37A mutant, apo form
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: 2.23 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

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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)65,06210
Polymers64,2332
Non-polymers8288
Water4,558253
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3644
Polymers32,1171
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6986
Polymers32,1171
Non-polymers5815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.298, 55.540, 120.676
Angle α, β, γ (deg.)90.00, 129.63, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
1ens_1
2ens_1
3ens_1

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
21ens_1(chain "A" and (resid 2 through 80 or (resid 81...
31ens_1(chain "B" and (resid 2 through 78 or (resid 79...

NCS oper: (Code: given
Matrix: (-0.025669, -0.042403, 0.998771), (0.029769, -0.998689, -0.041635), (0.999227, 0.028663, 0.026898)
Vector: 3.53667, -27.73226, 5.07726)

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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: 32116.523 Da / Num. of mol.: 2 / Mutation: D37A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#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.: 253 / 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: 3.45 Å3/Da / Density % sol: 64.35 %
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 Hepes (pH 7.5), 0.2 M Li2SO4, 25% 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: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.23→92.948 Å / Num. obs: 41670 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.67 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.226 / Net I/σ(I): 3
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.188 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2064 / CC1/2: 0.329 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→64.43 Å / SU ML: 0.363 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.337
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.281 1996 4.91 %
Rwork0.229 --
obs0.232 40669 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.15 Å2
Refinement stepCycle: LAST / Resolution: 2.23→64.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 42 253 4490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084362
X-RAY DIFFRACTIONf_angle_d1.0065951
X-RAY DIFFRACTIONf_dihedral_angle_d5.592595
X-RAY DIFFRACTIONf_chiral_restr0.053637
X-RAY DIFFRACTIONf_plane_restr0.008766
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDTypeAuth asym-ID
ens_11X-RAY DIFFRACTIONPOSITIONAL
ens_12X-RAY DIFFRACTIONPOSITIONALA
ens_13X-RAY DIFFRACTIONPOSITIONALB
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.290.3551270.29622324X-RAY DIFFRACTION84
2.29-2.350.32241300.27552523X-RAY DIFFRACTION89
2.35-2.420.29991500.25692712X-RAY DIFFRACTION96
2.42-2.50.36061550.24932729X-RAY DIFFRACTION97
2.5-2.590.28611570.2572766X-RAY DIFFRACTION99
2.59-2.690.35751450.27782833X-RAY DIFFRACTION100
2.69-2.810.36841420.25942829X-RAY DIFFRACTION100
2.81-2.960.31281270.25782843X-RAY DIFFRACTION100
2.96-3.150.2841400.2512842X-RAY DIFFRACTION100
3.15-3.390.30321440.24592819X-RAY DIFFRACTION99
3.39-3.730.26591610.20882815X-RAY DIFFRACTION99
3.73-4.270.2621270.18722864X-RAY DIFFRACTION99
4.27-5.380.20611510.19252838X-RAY DIFFRACTION99
5.38-64.430.23081400.20812936X-RAY DIFFRACTION99

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