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

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Basic information

Entry
Database: PDB / ID: 4jzt
TitleCrystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH (E68A mutant) bound to GTP
ComponentsdGTP pyrophosphohydrolase
KeywordsHYDROLASE / Nudix hydrolase / RNA pyrophosphohydrolase / RppH / cytosol
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
GUANOSINE-5'-TRIPHOSPHATE / Putative 8-oxo-dGTP diphosphatase YtkD
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Derived calculations
Revision 1.2Jul 10, 2013Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dGTP pyrophosphohydrolase
D: dGTP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8303
Polymers41,3072
Non-polymers5231
Water30617
1
A: dGTP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1772
Polymers20,6541
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: dGTP pyrophosphohydrolase


Theoretical massNumber of molelcules
Total (without water)20,6541
Polymers20,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.652, 117.652, 55.605
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 20653.582 Da / Num. of mol.: 2 / Mutation: E68A
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: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.3
Details: 1.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, 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: Sep 30, 2011
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: 2.9→48.81 Å / Num. all: 9913 / Num. obs: 9913 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 26.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1422 / % possible all: 100

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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: 2.9→48.81 Å / Cor.coef. Fo:Fc: 0.9215 / Cor.coef. Fo:Fc free: 0.8968 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 476 4.81 %RANDOM
Rwork0.2136 ---
obs0.2151 9904 100 %-
Displacement parametersBiso max: 191.69 Å2 / Biso mean: 82.0431 Å2 / Biso min: 45.61 Å2
Baniso -1Baniso -2Baniso -3
1--4.6362 Å20 Å20 Å2
2---4.6362 Å20 Å2
3---9.2724 Å2
Refine analyzeLuzzati coordinate error obs: 0.479 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 32 17 2655
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d973SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes388HARMONIC5
X-RAY DIFFRACTIONt_it2706HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2831SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2706HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg3644HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion20.36
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2912 138 4.96 %
Rwork0.2557 2647 -
all0.2575 2785 -
obs--100 %
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)
14.9834-0.7023-1.84542.71340.73395.58740.0620.0812-0.2856-0.1912-0.0723-0.0080.15730.080.0103-0.18670.0189-0.0274-0.06310.0072-0.0993.407845.8165-13.1458
22.52920.902-1.42232.8667-0.28745.0705-0.0039-0.0522-0.14640.2678-0.0271-0.0105-0.19950.09630.031-0.2187-0.07740.00810.04930.1161-0.0869-12.668848.580514.0576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 158
2X-RAY DIFFRACTION2{ D|* }D1 - 158

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