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

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Basic information

Entry
Database: PDB / ID: 4jzv
TitleCrystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - second 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-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 / 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 ...Nucleoside triphosphatase YtkD / 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
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: 2.2 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_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_asym_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_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.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_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)38,1957
Polymers37,8843
Non-polymers3114
Water1,26170
1
A: RNA PYROPHOSPHOHYDROLASE
C: RNA (5'-R(*(GCP)P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6315
Polymers19,3442
Non-polymers2873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-24 kcal/mol
Surface area8740 Å2
MethodPISA
2
B: RNA PYROPHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5652
Polymers18,5401
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.158, 138.025, 35.684
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / 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: ID23-1 / Wavelength: 0.972
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2012
RadiationMonochromator: DIAMOND (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.2→69.01 Å / Num. obs: 16071 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 95.1

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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
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF BSRPPH E68A

Resolution: 2.2→28.34 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 825 5.15 %RANDOM
Rwork0.22 ---
obs0.221 16024 98.2 %-
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.3936 Å20 Å20 Å2
2--3.9511 Å20 Å2
3----0.5576 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 37 18 70 2683
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072675HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.943600HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d965SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes364HARMONIC5
X-RAY DIFFRACTIONt_it2675HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.91
X-RAY DIFFRACTIONt_other_torsion19.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2789SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2566 147 5.33 %
Rwork0.2497 2613 -
all0.25 2760 -
obs--98.24 %
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)
12.58991.23530.50967.80721.13442.534-0.04080.0559-0.11820.1254-0.06990.14450.4097-0.02040.1106-0.1064-0.04240.0014-0.1165-0.0116-0.1053-12.390218.0495-10.0626
22.7346-0.3533-0.055111.5019-1.79653.68740.0850.0157-0.0843-0.69070.05660.49860.5442-0.2718-0.1416-0.0908-0.0372-0.0407-0.1174-0.0127-0.179917.465417.34386.7226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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