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- PDB-4s2w: Structure of E. coli RppH bound to sulfate ions -

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Basic information

Entry
Database: PDB / ID: 4s2w
TitleStructure of E. coli RppH bound to sulfate ions
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
RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.992 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 / 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 / _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

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Assembly

Deposited unit
A: RNA pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5427
Polymers18,9661
Non-polymers5766
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA pyrophosphohydrolase
hetero molecules

A: RNA pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,08414
Polymers37,9322
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3290 Å2
ΔGint-160 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.391, 38.851, 56.806
Angle α, β, γ (deg.)90.00, 98.95, 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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.4 M ammonium sulfate, 12% PEG 3350, 10% glycerol, 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: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.992→20 Å / Num. all: 11316 / Num. obs: 10978 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.87 / Num. unique all: 1578 / % possible all: 84.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.992→19.425 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 549 5 %RANDOM
Rwork0.1702 ---
all0.1724 10977 --
obs0.1724 10977 93.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.992→19.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 30 91 1385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071328
X-RAY DIFFRACTIONf_angle_d1.0981804
X-RAY DIFFRACTIONf_dihedral_angle_d13.032473
X-RAY DIFFRACTIONf_chiral_restr0.042182
X-RAY DIFFRACTIONf_plane_restr0.006228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9916-2.19180.27151270.2032413X-RAY DIFFRACTION87
2.1918-2.50840.23271350.19172575X-RAY DIFFRACTION93
2.5084-3.15810.22681410.18642667X-RAY DIFFRACTION95
3.1581-19.42640.19571460.15182773X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.71293.84714.28843.71672.41425.54460.2165-0.28010.66910.7768-0.2486-0.111-0.15810.3495-0.00130.4363-0.0776-0.04410.3402-0.00550.380521.42147.128117.3967
21.3801-1.48650.41571.977-0.69272.8067-0.1101-0.48780.20040.11520.11790.04120.2121-0.2764-0.02450.2609-0.06770.00950.23150.00640.243315.0084-8.64958.8145
32.646-0.35670.01352.33070.45672.29760.1432-0.08720.1660.0205-0.1742-0.053-0.2059-0.16020.02370.2292-0.0020.00450.17380.01640.222714.67997.60715.8513
42.3251.43711.43711.81850.49333.85730.1373-1.08730.3010.2354-0.4225-0.023-1.1911-0.81170.01740.75480.07840.01310.597-0.04410.337516.07796.202522.8574
53.55063.33820.16048.24090.96143.5902-0.53730.6708-0.0634-0.04130.1735-0.8794-0.46570.81270.12420.3798-0.06-0.14640.67420.16020.600531.37471.312323.5542
61.4793-0.30570.08062.01240.34641.82410.0173-0.2636-0.08910.1942-0.086-0.01340.0679-0.14970.00720.1927-0.0615-0.00740.22180.0240.203314.4176-3.77977.9874
75.6504-1.00490.82592.2395-0.76111.83540.1752-0.9243-0.19420.34480.28920.39250.232-0.9286-0.13380.331-0.12110.05080.67120.10650.32857.4004-3.099718.9085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 94 )
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 138 )
7X-RAY DIFFRACTION7chain 'A' and (resid 139 through 161 )

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