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- PDB-4s2v: E. coli RppH structure, KI soak -

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Basic information

Entry
Database: PDB / ID: 4s2v
TitleE. coli RppH structure, KI soak
ComponentsRNA pyrophosphohydrolase
KeywordsHYDROLASE / Nudix hydrolase / RNA pyrophosphohydrolase
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
ACETATE ION / IODIDE ION / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,14930
Polymers18,6231
Non-polymers3,52629
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.693, 59.693, 81.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18623.379 Da / Num. of mol.: 1
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: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, pH 8.0, 1.5 M K-acetate, 5% (v/v) glycerol and 20 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 15, 2012
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 35864 / Num. obs: 35292 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 3.54 / Num. unique all: 5563 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.539 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 1758 4.98 %RANDOM
Rwork0.1607 ---
all0.1627 35287 --
obs0.1627 35287 98.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 32 112 1307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041244
X-RAY DIFFRACTIONf_angle_d0.9721685
X-RAY DIFFRACTIONf_dihedral_angle_d13.064466
X-RAY DIFFRACTIONf_chiral_restr0.059168
X-RAY DIFFRACTIONf_plane_restr0.003215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.74610.23911340.18962517X-RAY DIFFRACTION95
1.7461-1.79740.22561270.18232498X-RAY DIFFRACTION97
1.7974-1.85540.24861390.17312601X-RAY DIFFRACTION97
1.8554-1.92160.23391280.16682522X-RAY DIFFRACTION98
1.9216-1.99850.21011320.15292579X-RAY DIFFRACTION98
1.9985-2.08930.18941360.14922551X-RAY DIFFRACTION98
2.0893-2.19940.22141400.15192641X-RAY DIFFRACTION99
2.1994-2.3370.20791320.15652524X-RAY DIFFRACTION99
2.337-2.5170.19911340.16322608X-RAY DIFFRACTION99
2.517-2.76970.21381410.16922630X-RAY DIFFRACTION100
2.7697-3.1690.21731340.16662633X-RAY DIFFRACTION100
3.169-3.98710.17751400.15272610X-RAY DIFFRACTION100
3.9871-19.54040.16821410.15812615X-RAY DIFFRACTION100

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