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- PDB-3ef5: Structure of the RNA pyrophosphohydrolase BdRppH in complex with dGTP -

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Basic information

Entry
Database: PDB / ID: 3ef5
TitleStructure of the RNA pyrophosphohydrolase BdRppH in complex with dGTP
ComponentsProbable pyrophosphohydrolase
KeywordsHYDROLASE / Nudix / RNA pyrophosphohydrolase
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2834
Polymers35,2692
Non-polymers1,0142
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-7 kcal/mol
Surface area13250 Å2
Unit cell
Length a, b, c (Å)68.446, 68.448, 92.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: PEG 4000, Na acetate, pH 7, 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: Aug 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.37 Å / Num. obs: 15730 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.049 / Χ2: 0.827 / Net I/σ(I): 32.267
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.494.40.6916950.821140.7
2.49-2.594.70.58311260.726164.5
2.59-2.75.60.53515120.904188.3
2.7-2.856.50.44817050.881196.9
2.85-3.027.20.23317290.8991100
3.02-3.267.30.14717630.9011100
3.26-3.587.30.07117530.8221100
3.58-4.17.30.0417500.7721100
4.1-5.177.20.02817990.7391100
5.17-506.70.02718980.772199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementResolution: 2.6→46.37 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.3 / WRfactor Rwork: 0.244 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.766 / SU B: 23.858 / SU ML: 0.255 / SU R Cruickshank DPI: 0.502 / SU Rfree: 0.344 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.473 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.297 686 5 %RANDOM
Rwork0.24 ---
obs0.243 13703 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.09 Å2 / Biso mean: 58.584 Å2 / Biso min: 46.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2--2.57 Å20 Å2
3----4.72 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 62 44 2237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212256
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.993062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20624.019107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.39815392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6651513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021691
X-RAY DIFFRACTIONr_nbd_refined0.2110.2882
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21420
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.24
X-RAY DIFFRACTIONr_mcbond_it0.4391.51338
X-RAY DIFFRACTIONr_mcangle_it0.74722061
X-RAY DIFFRACTIONr_scbond_it1.09231103
X-RAY DIFFRACTIONr_scangle_it1.7964.51001
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 40 -
Rwork0.357 844 -
all-884 -
obs--87.7 %
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)
16.9922-0.73832.748715.09285.38023.2220.5028-0.37280.8298-0.0226-0.7551-1.6284-0.02690.93420.25240.5016-0.1918-0.07230.66650.11740.503825.82-14.1664-11.619
24.7721-2.20641.65155.8748-0.53624.92480.113-0.09670.03680.03360.0157-0.20560.17050.3587-0.1287-0.1574-0.10160.0238-0.04410.0245-0.179817.0015-17.9579-15.2407
310.8664-0.4812-4.73469.652-3.54023.523-0.77450.35781.3372-0.66960.5348-0.2022-1.0054-0.07530.23970.4532-0.2208-0.26190.39020.15320.21821.94286.7909-12.2755
46.1113-2.2370.00814.9998-1.85224.63170.02020.01720.1501-0.12550.1111-0.0315-0.4139-0.1694-0.1312-0.0288-0.1033-0.0301-0.1694-0.0263-0.179-0.8379-0.1123-7.9333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 21
2X-RAY DIFFRACTION1A40 - 49
3X-RAY DIFFRACTION1A90 - 96
4X-RAY DIFFRACTION1A112 - 118
5X-RAY DIFFRACTION1A148 - 151
6X-RAY DIFFRACTION2A22 - 39
7X-RAY DIFFRACTION2A50 - 89
8X-RAY DIFFRACTION2A97 - 111
9X-RAY DIFFRACTION2A119 - 147
10X-RAY DIFFRACTION3B20 - 21
11X-RAY DIFFRACTION3B40 - 42
12X-RAY DIFFRACTION3B47 - 49
13X-RAY DIFFRACTION3B90 - 96
14X-RAY DIFFRACTION3B112 - 118
15X-RAY DIFFRACTION3B148 - 152
16X-RAY DIFFRACTION4B22 - 39
17X-RAY DIFFRACTION4B50 - 89
18X-RAY DIFFRACTION4B97 - 111
19X-RAY DIFFRACTION4B119 - 147

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