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- PDB-3ees: Structure of the RNA pyrophosphohydrolase BdRppH -

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Basic information

Entry
Database: PDB / ID: 3ees
TitleStructure of the RNA pyrophosphohydrolase BdRppH
ComponentsProbable pyrophosphohydrolase
KeywordsHYDROLASE / Nudix / RNA pyrophosphohydrolase
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / GTP binding / identical protein binding / metal ion binding
Similarity search - Function
Mutator MutT / : / MutY, C-terminal / NUDIX domain / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. ...Mutator MutT / : / MutY, C-terminal / NUDIX domain / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsMessing, S.A. / Gabelli, S.B. / Amzel, L.M.
CitationJournal: Structure / Year: 2009
Title: Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.
Authors: Messing, S.A. / Gabelli, S.B. / Liu, Q. / Celesnik, H. / Belasco, J.G. / Pineiro, S.A. / Amzel, L.M.
History
DepositionSep 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable pyrophosphohydrolase
B: Probable pyrophosphohydrolase


Theoretical massNumber of molelcules
Total (without water)35,2692
Polymers35,2692
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.491, 70.491, 100.481
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsGel filtration was used to determine the biological assembly.

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Components

#1: Protein Probable pyrophosphohydrolase


Mass: 17634.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: HD100 / Gene: mutT, Bd0714 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6MPX4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4
Details: PEG 4000, Na acetate, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: adsc Q210 / Detector: CCD / Date: Apr 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 63.36 / Number: 152495 / Rmerge(I) obs: 0.054 / Χ2: 1.55 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 22693 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095096.610.0362.1377
3.254.0999.410.0412.0487.2
2.843.2510010.0651.9387.1
2.582.8499.910.0991.67.2
2.392.5810010.1561.4487.2
2.252.3999.910.2171.357.1
2.142.2510010.3021.2477.1
2.052.1410010.4691.177
1.972.0598.810.6941.146.2
1.91.9792.110.8651.0473.8
ReflectionResolution: 1.9→33.26 Å / Num. obs: 23316 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.043 / Χ2: 1.273 / Net I/σ(I): 63.364
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9790.3922880.982100
1.97-2.05100.3323000.858100
2.05-2.14100.21423160.954100
2.14-2.259.90.16622841.318100
2.25-2.399.80.12723131.28699.9
2.39-2.589.90.08223091.11999.9
2.58-2.84100.05523451.124100
2.84-3.2510.20.0423441.323100
3.25-4.0910.60.03423761.70499.9
4.09-50100.03324411.93998

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Phasing

PhasingMethod: MIR
Phasing MIRResolution: 2.7→50 Å / FOM: 0.49 / Reflection: 8125
Phasing MIR der
IDDer set-ID
11
21
31
41
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1141.1236U0.43830.7130.07260.175
1260U0.80390.07690.12170.2666
134.9224U0.28230.93220.03010.0351
2160Hg0.26140.91670.02090.1744
2212.4028Hg0.3360.95270.04370.0516
2360Hg0.80360.41740.10710.0935
2418.1562Hg0.86870.43790.13490.0556
3143.8922Ho0.81570.08360.11890.1036
3239.7193Ho0.42490.70580.06020.0954
3314.5451Ho0.28160.39910.11820.0428
4152.028Sm0.79360.06060.11270.1192
Phasing MIR shell
Resolution (Å)FOMReflection
9.74-500.67396
6.14-9.740.68681
4.8-6.140.57844
4.07-4.80.531027
3.59-4.070.471140
3.25-3.590.471257
2.99-3.250.431349
2.79-2.990.391431

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MIR / Resolution: 1.9→33.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.795 / SU B: 8.251 / SU ML: 0.122 / SU R Cruickshank DPI: 0.178 / SU Rfree: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1188 5.1 %RANDOM
Rwork0.222 ---
obs0.223 23229 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.54 Å2 / Biso mean: 40.295 Å2 / Biso min: 25.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 0 107 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222162
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9592918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53324.135104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79415390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7541512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021640
X-RAY DIFFRACTIONr_nbd_refined0.190.2846
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.212
X-RAY DIFFRACTIONr_mcbond_it0.6771.51341
X-RAY DIFFRACTIONr_mcangle_it1.08322043
X-RAY DIFFRACTIONr_scbond_it1.6763978
X-RAY DIFFRACTIONr_scangle_it2.5814.5875
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 96 -
Rwork0.276 1601 -
all-1697 -
obs--100 %

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