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

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Basic information

Entry
Database: PDB / ID: 4jzs
TitleCrystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH (E68A mutant)
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
Putative 8-oxo-dGTP diphosphatase YtkD
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / MAD / 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 1.1Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,5453
Polymers41,3072
Non-polymers2381
Water1,04558
1
A: dGTP pyrophosphohydrolase


Theoretical massNumber of molelcules
Total (without water)20,6541
Polymers20,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: dGTP pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8922
Polymers20,6541
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.920, 116.920, 55.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6653.7
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion8.31.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, vapor diffusion, temperature 293K
2932vapor diffusion8.31.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, soaking in 500 mM NaI during 30s, vapor diffusion, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.9334
SYNCHROTRONESRF ID14-120.9334
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDSep 30, 2011
ADSC QUANTUM 2102CCDSep 30, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DIAMOND (1 1 1)SINGLE WAVELENGTHMx-ray1
2DIAMOND (1 1 1)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.2→48.72 Å / Num. all: 22194 / Num. obs: 22172 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.87 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2 / Num. unique all: 17999 / % possible all: 99.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHARPphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→37.43 Å / Cor.coef. Fo:Fc: 0.9395 / Cor.coef. Fo:Fc free: 0.9188 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1132 5.11 %RANDOM
Rwork0.2126 ---
obs0.2142 22157 99.78 %-
Displacement parametersBiso max: 155.61 Å2 / Biso mean: 59.5809 Å2 / Biso min: 33.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.0839 Å20 Å20 Å2
2--2.0839 Å20 Å2
3----4.1678 Å2
Refine analyzeLuzzati coordinate error obs: 0.375 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 15 58 2679
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d969SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes372HARMONIC5
X-RAY DIFFRACTIONt_it2685HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion318SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2807SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2685HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3608HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion19.17
LS refinement shellResolution: 2.2→2.31 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.221 142 4.89 %
Rwork0.2188 2760 -
all0.2189 2902 -
obs--99.78 %
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)
11.8576-1.2672-1.29583.7770.58585.25310.0841-0.0501-0.07140.0266-0.01730.1205-0.3481-0.5666-0.0668-0.09220.11890.0019-0.12720.0006-0.186337.884925.877810.916
22.2570.4363-0.62342.8720.53344.5556-0.26610.176-0.1147-0.01090.10910.11930.3492-0.07740.15690.08990.02280.0088-0.2528-0.0418-0.19648.522613.1203-16.2536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|158 }A1 - 158
2X-RAY DIFFRACTION2{ D|1 - D|158 }D1 - 158

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