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- PDB-4jzu: Crystal structure of the Bacillus subtilis pyrophosphohydrolase B... -

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Basic information

Entry
Database: PDB / ID: 4jzu
TitleCrystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - first guanosine residue in guanosine binding pocket
Components
  • RNA (5'-R(*(GCP)P*G)-3')
  • RNA PYROPHOSPHOHYDROLASE
KeywordsHYDROLASE/RNA / Nudix hydrolase / RNA pyrophosphohydrolase / RppH / cytosol / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside triphosphatase YtkD / 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 ...Nucleoside triphosphatase YtkD / 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 / Putative 8-oxo-dGTP diphosphatase YtkD
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsPiton, J. / Larue, V. / Thillier, Y. / Dorleans, A. / Pellegrini, O. / Li de la Sierra-Gallay, I. / Vasseur, J.J. / Debart, F. / Tisne, C. / Condon, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.
Authors: Piton, J. / Larue, V. / Thillier, Y. / Dorleans, A. / Pellegrini, O. / Li de la Sierra-Gallay, I. / Vasseur, J.J. / Debart, F. / Tisne, C. / Condon, C.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA PYROPHOSPHOHYDROLASE
B: RNA PYROPHOSPHOHYDROLASE
C: RNA (5'-R(*(GCP)P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1224
Polymers37,8843
Non-polymers2381
Water3,945219
1
A: RNA PYROPHOSPHOHYDROLASE
C: RNA (5'-R(*(GCP)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)19,3442
Polymers19,3442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7792
Polymers18,5401
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.377, 137.288, 34.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RNA PYROPHOSPHOHYDROLASE / 8-oxo-dGTPase / 7 / 8-dihydro-8-oxoguanine-triphosphatase / dGTP pyrophosphohydrolase


Mass: 18540.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU30630, mutTA, ytkD / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O35013, 8-oxo-dGTP diphosphatase
#2: RNA chain RNA (5'-R(*(GCP)P*G)-3')


Mass: 803.441 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.87 Å3/Da / Density % sol: 34.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM Hepes pH 7.5, 25% PEG 1000, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2012
RadiationMonochromator: DIAMOND (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.7→45.76 Å / Num. all: 31819 / Num. obs: 30642 / % possible obs: 96.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 23.3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4543 / % possible all: 90.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF BSRPPH E68A

Resolution: 1.7→21.44 Å / Cor.coef. Fo:Fc: 0.9616 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1553 5.08 %RANDOM
Rwork0.1827 ---
obs0.184 30581 95.03 %-
Displacement parametersBiso max: 140.43 Å2 / Biso mean: 39.8196 Å2 / Biso min: 20.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.6258 Å20 Å20 Å2
2--2.0339 Å20 Å2
3---0.5918 Å2
Refine analyzeLuzzati coordinate error obs: 0.231 Å
Refinement stepCycle: LAST / Resolution: 1.7→21.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 36 15 219 2820
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d963SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes364HARMONIC5
X-RAY DIFFRACTIONt_it2670HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion310SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3210SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2670HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg3592HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion4.52
X-RAY DIFFRACTIONt_other_torsion18.31
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2788 121 4.84 %
Rwork0.2174 2378 -
all0.2204 2499 -
obs--95.03 %
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)
11.8812-0.38730.46891.92-0.53221.57620.0353-0.1649-0.14470.00180.06840.11620.0549-0.1599-0.1037-0.0752-0.0128-0.0037-0.07920.0177-0.071612.068619.981210.2258
21.44521.40570.21945.24680.61340.9812-0.04690.0061-0.26870.080.1325-0.31080.14370.0381-0.0857-0.0342-0.0157-0.0009-0.0944-0.0051-0.0735-17.017215.7062-6.3702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 157
2X-RAY DIFFRACTION2{ B|* }B1 - 156

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