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- PDB-6vcr: Crystal structure of E.coli RppH in complex with CTP -

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Basic information

Entry
Database: PDB / ID: 6vcr
TitleCrystal structure of E.coli RppH in complex with CTP
ComponentsRNA pyrophosphohydrolase
KeywordsRNA BINDING PROTEIN / RNA degradation
Function / homology
Function and homology information


RNA NAD-cap (NMN-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / RNA decapping / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / cytoplasm
Similarity search - Function
RNA pyrophosphohydrolase RppH / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...RNA pyrophosphohydrolase RppH / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / PYROPHOSPHATE / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli S88 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM112940 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Authors: Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A.
History
DepositionDec 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,6896
Polymers18,9661
Non-polymers1,7245
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.525, 38.811, 57.692
Angle α, β, γ (deg.)90.000, 99.022, 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

#1: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase / Ap5A pyrophosphatase


Mass: 18965.773 Da / Num. of mol.: 1 / Mutation: Q159A, E160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli S88 (bacteria) / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.4 M (NH4)2SO4, 10% (v/v) PEG3350, 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→19.31 Å / Num. obs: 22689 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.5
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 2121 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2Y

4s2y


Resolution: 1.6→19.31 Å / SU ML: 0.1385 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7848
RfactorNum. reflection% reflection
Rfree0.1904 1135 5 %
Rwork0.1643 --
obs0.1656 22688 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1302 0 97 186 1585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791436
X-RAY DIFFRACTIONf_angle_d1.33991967
X-RAY DIFFRACTIONf_chiral_restr0.0528198
X-RAY DIFFRACTIONf_plane_restr0.006235
X-RAY DIFFRACTIONf_dihedral_angle_d18.9937533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.23741350.20212555X-RAY DIFFRACTION94.22
1.67-1.760.22631400.18972672X-RAY DIFFRACTION99.5
1.76-1.870.20671420.17432690X-RAY DIFFRACTION99.93
1.87-2.020.20271420.16452696X-RAY DIFFRACTION99.89
2.02-2.220.19981420.15362704X-RAY DIFFRACTION99.96
2.22-2.540.19421430.15862713X-RAY DIFFRACTION99.83
2.54-3.20.16431440.16512736X-RAY DIFFRACTION99.83
3.2-19.310.1871470.16082787X-RAY DIFFRACTION99.69

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