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- PDB-6vcn: Crystal structure of E.coli RppH in complex with ppcpG -

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Basic information

Entry
Database: PDB / ID: 6vcn
TitleCrystal structure of E.coli RppH in complex with ppcpG
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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)19,8706
Polymers18,9651
Non-polymers9055
Water2,108117
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)61.796, 61.796, 72.311
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

21A-392-

HOH

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Components

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


Mass: 18964.723 Da / Num. of mol.: 1 / Mutation: K149A, E150A
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-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.5 M NH4Cl, 10% (v/v) PEG4000

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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 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.48 Å / Num. obs: 12944 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.98 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 1244 / CC1/2: 0.718

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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: 1.9→19.48 Å / SU ML: 0.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.7136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 648 5.01 %
Rwork0.1996 12295 -
obs0.2023 12943 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 52 117 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01281390
X-RAY DIFFRACTIONf_angle_d1.29251891
X-RAY DIFFRACTIONf_chiral_restr0.07186
X-RAY DIFFRACTIONf_plane_restr0.0075234
X-RAY DIFFRACTIONf_dihedral_angle_d19.4044502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.31351260.2362389X-RAY DIFFRACTION99.25
2.05-2.250.26121280.21282426X-RAY DIFFRACTION99.96
2.25-2.580.28211290.21432457X-RAY DIFFRACTION100
2.58-3.250.27651300.20392463X-RAY DIFFRACTION99.96
3.25-19.480.21351350.18022560X-RAY DIFFRACTION99.63

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