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- PDB-7sp3: E. coli RppH bound to Ap4A -

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Basic information

Entry
Database: PDB / ID: 7sp3
TitleE. coli RppH bound to Ap4A
ComponentsRNA pyrophosphohydrolase
KeywordsRNA BINDING PROTEIN / Cap / Ap4A / RppH / Nudix hydrolase
Function / homology
Function and homology information


mRNA 5'-diphosphatase activity / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cytoplasm
Similarity search - Function
RNA pyrophosphohydrolase RppH / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / FLUORIDE ION / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSerganov, A.A. / Vasilyev, N. / Nuthanakanti, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112940 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: A distinct RNA recognition mechanism governs Np 4 decapping by RppH.
Authors: Levenson-Palmer, R. / Luciano, D.J. / Vasilyev, N. / Nuthanakanti, A. / Serganov, A. / Belasco, J.G.
History
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9307
Polymers18,9661
Non-polymers9646
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.390, 36.384, 57.801
Angle α, β, γ (deg.)90.000, 102.101, 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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase


Mass: 18965.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rppH, nudH, D9D94_13650, D9E88_05455, D9J61_06705, G5V60_04980, GP711_07030
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A3K0QF38, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 118 molecules

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


Mass: 836.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O19P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.4 M (NH4)2SO4, 10% (v/v) PEG3350, and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→19.4 Å / Num. obs: 20993 / % possible obs: 97.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 18.88 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.021 / Rrim(I) all: 0.048 / Net I/σ(I): 22.49
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5874 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1890 / CC1/2: 0.752 / CC star: 0.926 / Rpim(I) all: 0.3048 / Rrim(I) all: 0.6652 / % possible all: 89.32

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
CrystalCleardata collection
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2W

4s2w


Resolution: 1.6→18.84 Å / SU ML: 0.197 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.9407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2195 1050 5 %
Rwork0.1828 19941 -
obs0.1846 20991 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.77 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 41 112 1376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681378
X-RAY DIFFRACTIONf_angle_d0.95671885
X-RAY DIFFRACTIONf_chiral_restr0.0563192
X-RAY DIFFRACTIONf_plane_restr0.0059237
X-RAY DIFFRACTIONf_dihedral_angle_d17.7511188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.30831390.25672635X-RAY DIFFRACTION91.46
1.68-1.790.26841470.22252789X-RAY DIFFRACTION96.83
1.79-1.930.26441490.20922848X-RAY DIFFRACTION97.46
1.93-2.120.22621500.18822850X-RAY DIFFRACTION98.26
2.12-2.430.23811540.18672910X-RAY DIFFRACTION99.06
2.43-3.060.22591530.18252910X-RAY DIFFRACTION99.71
3.06-18.840.18511580.16252999X-RAY DIFFRACTION99.87

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