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- PDB-7ody: Cyanophage S-2L MazG-like pyrophosphohydrolase bound to dGDP and ... -

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Basic information

Entry
Database: PDB / ID: 7ody
TitleCyanophage S-2L MazG-like pyrophosphohydrolase bound to dGDP and three catalytic Mn2+ ions per active site
ComponentsMazG-like pyrophosphohydrolase (MazZ)
KeywordsVIRAL PROTEIN / S-2L / MazG-like pyrophosphohydrolase / MazZ
Function / homologyMazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesCyanophage S-2L (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 Å
AuthorsCzernecki, D. / Delarue, M.
CitationJournal: Nat Commun / Year: 2021
Title: Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA.
Authors: Czernecki, D. / Bonhomme, F. / Kaminski, P.A. / Delarue, M.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MazG-like pyrophosphohydrolase (MazZ)
B: MazG-like pyrophosphohydrolase (MazZ)
C: MazG-like pyrophosphohydrolase (MazZ)
D: MazG-like pyrophosphohydrolase (MazZ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,08628
Polymers46,9494
Non-polymers3,13724
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19860 Å2
ΔGint-334 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.590, 91.370, 114.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
MazG-like pyrophosphohydrolase (MazZ)


Mass: 11737.292 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanophage S-2L (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-DGI / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE


Type: DNA linking / Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM Li2SO4; 1.26 M (NH4)2SO4; 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.127129 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 22, 2019 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127129 Å / Relative weight: 1
ReflectionResolution: 1.42919251276→48.52 Å / Num. obs: 104356 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 19.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.025 / Rrim(I) all: 0.093 / Net I/σ(I): 14.1
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.938 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7504 / CC1/2: 0.579 / Rpim(I) all: 0.605 / Rrim(I) all: 2.032 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.43→48.45 Å / SU ML: 0.1522 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1665 5210 5 %
Rwork0.1644 99022 -
obs0.1645 104232 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.67 Å2
Refinement stepCycle: LAST / Resolution: 1.43→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 160 488 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813133
X-RAY DIFFRACTIONf_angle_d1.34944302
X-RAY DIFFRACTIONf_chiral_restr0.2712514
X-RAY DIFFRACTIONf_plane_restr0.0057591
X-RAY DIFFRACTIONf_dihedral_angle_d13.76181196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.29211630.3013101X-RAY DIFFRACTION95.63
1.45-1.460.30881710.28283242X-RAY DIFFRACTION99.65
1.46-1.480.27811720.26163275X-RAY DIFFRACTION99.97
1.48-1.50.25521730.23773282X-RAY DIFFRACTION99.68
1.5-1.520.24491720.22413258X-RAY DIFFRACTION100
1.52-1.540.22591720.22093281X-RAY DIFFRACTION99.97
1.54-1.560.23591720.2173251X-RAY DIFFRACTION99.94
1.56-1.580.211720.20763285X-RAY DIFFRACTION99.97
1.58-1.610.2271720.20493279X-RAY DIFFRACTION100
1.61-1.640.21331720.20043271X-RAY DIFFRACTION100
1.64-1.660.20531730.20143279X-RAY DIFFRACTION99.97
1.66-1.690.21361720.20153264X-RAY DIFFRACTION100
1.69-1.730.22551740.19113312X-RAY DIFFRACTION100
1.73-1.760.18811720.18653268X-RAY DIFFRACTION100
1.76-1.80.17141720.1793273X-RAY DIFFRACTION100
1.8-1.840.1671730.17513293X-RAY DIFFRACTION99.97
1.84-1.890.18321720.17283283X-RAY DIFFRACTION100
1.89-1.940.15691750.16623313X-RAY DIFFRACTION100
1.94-20.16551730.16463291X-RAY DIFFRACTION99.97
2-2.060.16221740.1533305X-RAY DIFFRACTION100
2.06-2.130.14321750.14183325X-RAY DIFFRACTION100
2.13-2.220.14861730.14133293X-RAY DIFFRACTION100
2.22-2.320.13441740.13523302X-RAY DIFFRACTION100
2.32-2.440.13351750.13623333X-RAY DIFFRACTION100
2.44-2.60.13661760.13993329X-RAY DIFFRACTION100
2.6-2.80.14181760.13933344X-RAY DIFFRACTION99.97
2.8-3.080.15071760.15023345X-RAY DIFFRACTION99.94
3.08-3.520.15671770.15553373X-RAY DIFFRACTION100
3.52-4.440.14011800.14023417X-RAY DIFFRACTION100
4.44-48.450.19941870.1983555X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: 8.20772748975 Å / Origin y: -11.8002283633 Å / Origin z: -18.5610974181 Å
111213212223313233
T0.151654447776 Å20.0202662404363 Å20.0059334178108 Å2-0.144325978819 Å2-0.00316751924475 Å2--0.14902610441 Å2
L0.584411064795 °20.207692236125 °2-0.0426160006744 °2-0.680107749016 °2-0.23106683436 °2--0.746271215949 °2
S0.00340142423013 Å °0.0502501756744 Å °0.0202660109421 Å °-0.00594088541521 Å °-0.0278379116847 Å °-0.0188844825656 Å °-0.0439752121295 Å °0.00154535489073 Å °0.0221455592866 Å °
Refinement TLS groupSelection details: all

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