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- PDB-6zpb: Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and two ca... -

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Basic information

Entry
Database: PDB / ID: 6zpb
TitleCyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and two catalytic Co2+ ions
ComponentsDatZ
KeywordsVIRAL PROTEIN / S-2L / HD phosphohydrolase / DatZ
Function / homologyChem-3D1 / :
Function and homology information
Biological speciesCyanophage S-2L (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72097384171 Å
AuthorsCzernecki, D. / Legrand, P. / Delarue, M.
CitationJournal: Nat Commun / Year: 2021
Title: How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA.
Authors: Czernecki, D. / Legrand, P. / Tekpinar, M. / Rosario, S. / Kaminski, P.A. / Delarue, M.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 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: DatZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0415
Polymers20,6131
Non-polymers4284
Water4,684260
1
A: DatZ
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)126,24430
Polymers123,6766
Non-polymers2,56824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area22180 Å2
ΔGint-234 kcal/mol
Surface area40160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.827, 141.827, 53.725
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

21A-445-

HOH

31A-491-

HOH

41A-497-

HOH

51A-508-

HOH

61A-511-

HOH

71A-523-

HOH

81A-555-

HOH

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Components

#1: Protein DatZ


Mass: 20612.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanophage S-2L (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 1.5 M LiSO4; 100 mM HEPES; 10 mM CoCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 1.72→40.44 Å / Num. obs: 21613 / % possible obs: 98.4 % / Redundancy: 14.2 % / Biso Wilson estimate: 14.0930917762 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.022 / Rrim(I) all: 0.086 / Net I/σ(I): 25
Reflection shellResolution: 1.72→1.77 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 1400 / CC1/2: 0.939 / Rpim(I) all: 0.137 / Rrim(I) all: 0.338 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72097384171→40.4358636633 Å / SU ML: 0.165812802632 / Cross valid method: FREE R-VALUE / σ(F): 1.45045910224 / Phase error: 16.9899637983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.170205185922 1053 4.87522570489 %
Rwork0.146001949293 20546 -
obs0.147191339442 21599 98.2934376991 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.5063621561 Å2
Refinement stepCycle: LAST / Resolution: 1.72097384171→40.4358636633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 21 260 1676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01104299348321510
X-RAY DIFFRACTIONf_angle_d1.281938115782065
X-RAY DIFFRACTIONf_chiral_restr0.101106111192234
X-RAY DIFFRACTIONf_plane_restr0.00895704191404278
X-RAY DIFFRACTIONf_dihedral_angle_d18.1671548412582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.721-1.79930.2497408317191160.1860781328982312X-RAY DIFFRACTION89.4950239587
1.7993-1.89420.2301120808811300.1620568538592536X-RAY DIFFRACTION96.8398111151
1.8942-2.01280.2175767350141250.1519278678192582X-RAY DIFFRACTION99.9630723781
2.0128-2.16820.1747548669081300.1370713812442610X-RAY DIFFRACTION99.9635169646
2.1682-2.38640.1594869720591360.1424669767632589X-RAY DIFFRACTION99.9633162142
2.3864-2.73170.1497814554281370.1425662673062600X-RAY DIFFRACTION100
2.7317-3.44130.1849633681921380.1418039489772630X-RAY DIFFRACTION100
3.4413-40.43586366330.1393822486741410.1433023499932687X-RAY DIFFRACTION100

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