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- PDB-6zpc: Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dATP -

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Basic information

Entry
Database: PDB / ID: 6zpc
TitleCyanophage S-2L HD phosphohydrolase (DatZ) bound to dATP
ComponentsDatZ
KeywordsVIRAL PROTEIN / S-2L / HD phosphohydrolase / DatZ
Function / homology2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesCyanophage S-2L (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26835935206 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

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Assembly

Deposited unit
A: DatZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1835
Polymers20,6131
Non-polymers5704
Water4,161231
1
A: DatZ
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)127,09830
Polymers123,6766
Non-polymers3,42324
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 area24660 Å2
ΔGint-405 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.650, 141.650, 53.730
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-346-

HOH

21A-437-

HOH

31A-476-

HOH

41A-479-

HOH

51A-482-

HOH

61A-493-

HOH

71A-523-

HOH

81A-526-

HOH

91A-530-

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-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5 M LiSO4; 100 mM HEPES; 10 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 5, 2019 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.26835935206→40.89 Å / Num. obs: 54250 / % possible obs: 99.8 % / Redundancy: 19.5 % / Biso Wilson estimate: 15.8895422676 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.015 / Rrim(I) all: 0.068 / Net I/σ(I): 21.5
Reflection shellResolution: 1.26835935206→1.3 Å / Redundancy: 17.6 % / Rmerge(I) obs: 1.287 / Mean I/σ(I) obs: 2 / Num. unique obs: 3890 / CC1/2: 0.686 / Rpim(I) all: 0.312 / Rrim(I) all: 1.326 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.26835935206→40.4160912425 Å / SU ML: 0.168504395107 / Cross valid method: FREE R-VALUE / σ(F): 1.38654670294 / Phase error: 15.3389968306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.146081109347 2711 5.00027666599 %
Rwork0.125814610208 51506 -
obs0.126828745694 54217 99.7718113395 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.5874180448 Å2
Refinement stepCycle: LAST / Resolution: 1.26835935206→40.4160912425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 33 231 1659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007712596743381505
X-RAY DIFFRACTIONf_angle_d1.03351196582062
X-RAY DIFFRACTIONf_chiral_restr0.0677262197426236
X-RAY DIFFRACTIONf_plane_restr0.00731991570705272
X-RAY DIFFRACTIONf_dihedral_angle_d17.9793375773578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2684-1.29140.3426823972471370.348890845742604X-RAY DIFFRACTION96.7867231638
1.2914-1.31630.2710650735851430.3140935803582707X-RAY DIFFRACTION99.9298737728
1.3163-1.34310.2881652645291410.2913607656652677X-RAY DIFFRACTION99.5407983045
1.3431-1.37230.2324918361741440.26046999642715X-RAY DIFFRACTION99.8254189944
1.3723-1.40430.2692848593151390.2187869281062669X-RAY DIFFRACTION99.8222538215
1.4043-1.43940.240841419621430.1924912107212717X-RAY DIFFRACTION99.9650471863
1.4394-1.47830.2040574652131410.1585981221222690X-RAY DIFFRACTION99.9646892655
1.4783-1.52180.1556515239251430.1311055132462716X-RAY DIFFRACTION100
1.5218-1.57090.1497481523321420.1256216881422710X-RAY DIFFRACTION100
1.5709-1.62710.1441868400631430.1186888582362709X-RAY DIFFRACTION100
1.6271-1.69220.1315494783271420.1095898265832692X-RAY DIFFRACTION100
1.6922-1.76920.1342544855351430.09756989597962714X-RAY DIFFRACTION100
1.7692-1.86250.1264687060711430.09967803886532730X-RAY DIFFRACTION100
1.8625-1.97920.1254698159951430.09608501546772713X-RAY DIFFRACTION100
1.9792-2.1320.112925451221430.09386647302252723X-RAY DIFFRACTION100
2.132-2.34650.1099897514921440.09617974867252729X-RAY DIFFRACTION100
2.3465-2.6860.1224124657521440.1060509175692731X-RAY DIFFRACTION100
2.686-3.38390.1437973482791440.1198758402792751X-RAY DIFFRACTION100
3.3839-40.41609124250.1515024933371490.1351383770742809X-RAY DIFFRACTION99.8649561107

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