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- PDB-9ojp: Crystal structure of E. coli ApaH bound to Manganese ions -

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Basic information

Entry
Database: PDB / ID: 9ojp
TitleCrystal structure of E. coli ApaH bound to Manganese ions
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: 1.68 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

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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)65,64416
Polymers64,3212
Non-polymers1,32314
Water12,430690
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7518
Polymers32,1611
Non-polymers5907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8938
Polymers32,1611
Non-polymers7327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.067, 54.851, 120.527
Angle α, β, γ (deg.)90.000, 130.120, 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 28 or (resid 29...
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_11ALAALAARGARGAA2 - 1032 - 103
d_12GLNGLNGLYGLYAA105 - 190105 - 190
d_13LEULEUASPASPAA192 - 193192 - 193
d_14TYRTYRARGARGAA195 - 270195 - 270
d_21ALAALAARGARGBB2 - 1032 - 103
d_22GLNGLNGLYGLYBB105 - 190105 - 190
d_23LEULEUASPASPBB192 - 193192 - 193
d_24TYRTYRARGARGBB195 - 270195 - 270

NCS oper: (Code: givenMatrix: (-0.030152252396, -0.0506610186959, 0.998260638741), (0.0313349281133, -0.998271771236, -0.0497151187564), (0.999054034552, 0.0297814025447, 0.0316876017851)Vector: 3. ...NCS oper: (Code: given
Matrix: (-0.030152252396, -0.0506610186959, 0.998260638741), (0.0313349281133, -0.998271771236, -0.0497151187564), (0.999054034552, 0.0297814025447, 0.0316876017851)
Vector: 3.1333973426, -27.7355157596, 4.82030803154)

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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.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / 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.: 690 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 2 mM MnCl2, 25 mM Hepes (pH 7.5), 0.2 M NaCl. 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: APS / Beamline: 24-ID-E / Wavelength: 1.3625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3625 Å / Relative weight: 1
ReflectionResolution: 1.68→83.36 Å / Num. obs: 92329 / % possible obs: 96.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4091 / CC1/2: 0.665 / % possible all: 87

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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: 1.68→83.36 Å / SU ML: 0.1809 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4365
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1931 3846 2.17 %
Rwork0.1816 173147 -
obs0.1819 92329 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.47 Å2
Refinement stepCycle: LAST / Resolution: 1.68→83.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4210 0 64 690 4964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734409
X-RAY DIFFRACTIONf_angle_d0.95836016
X-RAY DIFFRACTIONf_chiral_restr0.0585638
X-RAY DIFFRACTIONf_plane_restr0.0249773
X-RAY DIFFRACTIONf_dihedral_angle_d12.9657600
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.563946015386 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.3281180.28835522X-RAY DIFFRACTION81.14
1.7-1.720.31331620.28196310X-RAY DIFFRACTION91.91
1.72-1.740.27651090.26436207X-RAY DIFFRACTION91.98
1.74-1.770.2721440.26186301X-RAY DIFFRACTION92.51
1.77-1.80.30471550.25976185X-RAY DIFFRACTION91.67
1.8-1.820.26861130.26066237X-RAY DIFFRACTION91.55
1.82-1.850.2611630.25116412X-RAY DIFFRACTION94.48
1.85-1.890.2641450.25296486X-RAY DIFFRACTION94.78
1.89-1.920.26571420.24856446X-RAY DIFFRACTION94.87
1.92-1.960.28781390.22876535X-RAY DIFFRACTION95.7
1.96-20.22741220.21976488X-RAY DIFFRACTION95.94
2-2.040.2041510.20466589X-RAY DIFFRACTION96.42
2.04-2.090.20831700.1956468X-RAY DIFFRACTION95.92
2.09-2.140.2291350.18146448X-RAY DIFFRACTION94.6
2.14-2.20.20671460.18296270X-RAY DIFFRACTION92.28
2.2-2.260.17681470.17486523X-RAY DIFFRACTION96.44
2.26-2.330.19671420.17556604X-RAY DIFFRACTION97.53
2.34-2.420.18151440.17046619X-RAY DIFFRACTION97.41
2.42-2.520.16711490.16236647X-RAY DIFFRACTION97.13
2.52-2.630.19161400.17056586X-RAY DIFFRACTION96.71
2.63-2.770.15091430.16976538X-RAY DIFFRACTION96.69
2.77-2.940.16561500.17136556X-RAY DIFFRACTION96.28
2.94-3.170.18491400.16236322X-RAY DIFFRACTION92.86
3.17-3.490.17171380.16156529X-RAY DIFFRACTION96.23
3.49-3.990.17051490.13546501X-RAY DIFFRACTION95.3
3.99-5.030.12271420.13796434X-RAY DIFFRACTION95.19
5.03-83.360.18091480.18096384X-RAY DIFFRACTION93.7

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