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- PDB-9olz: Crystal structure of E. coli ApaH in complex with Ap4A -

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Basic information

Entry
Database: PDB / ID: 9olz
TitleCrystal structure of E. coli ApaH in complex with Ap4A
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(ADENOSINE)-5'-TETRAPHOSPHATE / : / Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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)64,84311
Polymers62,6632
Non-polymers2,1799
Water8,449469
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3025
Polymers31,3321
Non-polymers9714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5416
Polymers31,3321
Non-polymers1,2095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.716, 55.321, 120.974
Angle α, β, γ (deg.)90.000, 129.880, 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_11ALAALAARGARGAA2 - 1032 - 103
d_12GLNGLNLYSLYSAA105 - 133105 - 133
d_13CYSCYSARGARGAA135 - 270135 - 270
d_21ALAALAARGARGBB2 - 1032 - 103
d_22GLNGLNLYSLYSBB105 - 133105 - 133
d_23CYSCYSARGARGBB135 - 270135 - 270

NCS oper: (Code: givenMatrix: (-0.0281364993886, -0.0506135166852, 0.99832189665), (0.0323857930984, -0.998239155516, -0.0496965672818), (0.999079325083, 0.0309331589556, 0.0297261142682)Vector: 3. ...NCS oper: (Code: given
Matrix: (-0.0281364993886, -0.0506135166852, 0.99832189665), (0.0323857930984, -0.998239155516, -0.0496965672818), (0.999079325083, 0.0309331589556, 0.0297261142682)
Vector: 3.34700818892, -27.7658337957, 4.994292836)

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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: 31331.666 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, 478 molecules

#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O19P4 / Feature type: SUBJECT OF INVESTIGATION
#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-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.: 469 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 5 mM MgCl2, 25 mM Hepes (pH 7.5), 0.2 M NaCl and soaked with Ap4A Well solution: 0.2 M Sodium malonate, 20% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.71→83.67 Å / Num. obs: 91253 / % possible obs: 98.3 % / Redundancy: 5 % / Biso Wilson estimate: 31.6 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 1.71→1.73 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.739 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4085 / CC1/2: 0.253 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→83.67 Å / SU ML: 0.2797 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 3835 2.21 %
Rwork0.1946 169809 -
obs0.1951 91253 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.89 Å2
Refinement stepCycle: LAST / Resolution: 1.71→83.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 91 469 4780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824463
X-RAY DIFFRACTIONf_angle_d1.11936103
X-RAY DIFFRACTIONf_chiral_restr0.0576647
X-RAY DIFFRACTIONf_plane_restr0.0073781
X-RAY DIFFRACTIONf_dihedral_angle_d22.1676645
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.576875335739 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.39941040.36784763X-RAY DIFFRACTION72.11
1.73-1.750.36631140.35766143X-RAY DIFFRACTION94.79
1.75-1.770.36251660.34666391X-RAY DIFFRACTION96.68
1.77-1.80.3541810.33296409X-RAY DIFFRACTION97.04
1.8-1.830.36341230.32586377X-RAY DIFFRACTION97.16
1.83-1.850.33091350.31256288X-RAY DIFFRACTION96.47
1.85-1.890.32271350.3136251X-RAY DIFFRACTION94.9
1.89-1.920.34781530.3336471X-RAY DIFFRACTION97.51
1.92-1.950.32131410.30326397X-RAY DIFFRACTION97.71
1.95-1.990.29591450.26996461X-RAY DIFFRACTION98.13
1.99-2.030.29511570.24216438X-RAY DIFFRACTION98.18
2.03-2.080.23771510.21956465X-RAY DIFFRACTION98.25
2.08-2.120.2421440.21256499X-RAY DIFFRACTION98.25
2.12-2.180.23821430.20886379X-RAY DIFFRACTION97.97
2.18-2.240.23641280.2066481X-RAY DIFFRACTION97.93
2.24-2.30.19951660.20576480X-RAY DIFFRACTION97.76
2.3-2.380.25721390.20196308X-RAY DIFFRACTION96.21
2.38-2.460.21641530.19466322X-RAY DIFFRACTION96.14
2.46-2.560.24111300.19016433X-RAY DIFFRACTION97.65
2.56-2.680.21831550.19786408X-RAY DIFFRACTION97.39
2.68-2.820.21191360.19436373X-RAY DIFFRACTION96.86
2.82-2.990.23761380.19786314X-RAY DIFFRACTION96.11
2.99-3.220.21351520.18716206X-RAY DIFFRACTION94.73
3.22-3.550.18391250.17896006X-RAY DIFFRACTION90.82
3.55-4.060.17021400.15086299X-RAY DIFFRACTION95.34
4.06-5.120.17221440.14666250X-RAY DIFFRACTION94.87
5.12-83.670.18581370.16876197X-RAY DIFFRACTION94.33

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