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- PDB-6vco: Crystal structure of E.coli RppH in complex with ppcpA -

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Basic information

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


RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / P-body / magnesium ion binding / cytoplasm
Similarity search - Function
RNA pyrophosphohydrolase RppH / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...RNA pyrophosphohydrolase RppH / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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)19,4712
Polymers18,9661
Non-polymers5051
Water2,756153
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)79.140, 38.955, 57.734
Angle α, β, γ (deg.)90.000, 100.064, 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 (strain K12) (bacteria)
Strain: K12 / 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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 6.25% (v/v) PEG3350, and 5% (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: May 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→19.48 Å / Num. obs: 18406 / % possible obs: 95.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 22.06 Å2 / CC1/2: 0.999 / Net I/σ(I): 24
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 1706 / CC1/2: 0.923

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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: 1.7→19.48 Å / SU ML: 0.1848 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.7444
RfactorNum. reflection% reflection
Rfree0.203 921 5 %
Rwork0.1717 --
obs0.1732 18402 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.57 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 31 153 1495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151379
X-RAY DIFFRACTIONf_angle_d1.19251871
X-RAY DIFFRACTIONf_chiral_restr0.065188
X-RAY DIFFRACTIONf_plane_restr0.0087233
X-RAY DIFFRACTIONf_dihedral_angle_d19.3389502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.24581220.21762316X-RAY DIFFRACTION90.36
1.79-1.90.27031280.20092432X-RAY DIFFRACTION93.29
1.9-2.050.22011300.18632461X-RAY DIFFRACTION94.53
2.05-2.250.20961300.17132479X-RAY DIFFRACTION95.36
2.25-2.580.20511340.16732548X-RAY DIFFRACTION96.65
2.58-3.250.21541350.17232559X-RAY DIFFRACTION97.89
3.25-19.480.181420.16182686X-RAY DIFFRACTION99.47

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