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- PDB-4s2x: Structure of E. coli RppH bound to RNA and two magnesium ions -

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Basic information

Entry
Database: PDB / ID: 4s2x
TitleStructure of E. coli RppH bound to RNA and two magnesium ions
Components
  • RNA (5'-R(*(APC)*GP*U)-3')
  • RNA pyrophosphohydrolase
Keywordshydrolase/RNA / Nudix hydrolase / RNA pyrophosphohydrolase / hydrolase-RNA complex
Function / homology
Function and homology information


RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / mRNA 5'-diphosphatase activity / RNA destabilization / 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 / 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
RNA / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVasilyev, N. / Serganov, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay.
Authors: Vasilyev, N. / Serganov, A.
History
DepositionJan 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA pyrophosphohydrolase
B: RNA (5'-R(*(APC)*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3006
Polymers20,0592
Non-polymers2414
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-141 kcal/mol
Surface area14680 Å2
Unit cell
Length a, b, c (Å)78.499, 38.868, 57.201
Angle α, β, γ (deg.)90.00, 100.13, 90.00
Int Tables number5
Space group name H-MC121

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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 (E. coli) / Strain: K12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: RNA chain RNA (5'-R(*(APC)*GP*U)-3')


Mass: 1093.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Prepared by in vitro transcription
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: crystal growth: 0.4 M ammonium sulfate, 12% PEG 3350, 10%glycerol. crystal soaking: 0.05 M MOPS-Na pH 7.0, 0.05 M ammonium sulfate, 0.05 M magnesium chloride, 15% PEG3350 and 25% ...Details: crystal growth: 0.4 M ammonium sulfate, 12% PEG 3350, 10%glycerol. crystal soaking: 0.05 M MOPS-Na pH 7.0, 0.05 M ammonium sulfate, 0.05 M magnesium chloride, 15% PEG3350 and 25% pentaerythritol propoxylate 5/4 PO/OH, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2013
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 26827 / Num. obs: 26252 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.041
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.65 / Num. unique all: 4066 / % possible all: 93

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.automr)model building
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4S2W

4s2w


Resolution: 1.5→19.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.851 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21592 1310 5 %RANDOM
Rwork0.18897 ---
all0.19034 24889 --
obs0.19034 24889 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0.82 Å2
2--1.48 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 54 12 109 1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191433
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.9451969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79723.47869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7521512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211112
X-RAY DIFFRACTIONr_rigid_bond_restr2.74131432
X-RAY DIFFRACTIONr_sphericity_free28.598533
X-RAY DIFFRACTIONr_sphericity_bonded18.38451468
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 90 -
Rwork0.45 1695 -
obs--91.68 %

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