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

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Basic information

Entry
Database: PDB / ID: 6zpa
TitleCyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and one catalytic Zn2+ ion
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: 0.860002552904 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)20,9364
Polymers20,6131
Non-polymers3243
Water3,927218
1
A: DatZ
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)125,61724
Polymers123,6766
Non-polymers1,94218
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 area21630 Å2
ΔGint-332 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.489, 141.489, 53.601
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-347-

HOH

21A-418-

HOH

31A-461-

HOH

41A-466-

HOH

51A-467-

HOH

61A-482-

HOH

71A-512-

HOH

81A-513-

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-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.: 1 / Source method: obtained synthetically / Formula: Li
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.5 M LiSO4; 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.729309 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2018 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729309 Å / Relative weight: 1
ReflectionResolution: 0.86→49.11 Å / Num. obs: 172371 / % possible obs: 100 % / Redundancy: 61.2 % / Biso Wilson estimate: 7.42892855759 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.013 / Rrim(I) all: 0.105 / Net I/σ(I): 27.6
Reflection shellResolution: 0.86→0.87 Å / Redundancy: 51.8 % / Rmerge(I) obs: 4.749 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8517 / CC1/2: 0.689 / Rpim(I) all: 0.667 / Rrim(I) all: 4.796 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography data reductionCrystal hits: 1 / Frame hits: 3 / Frames total: 9800

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 0.860002552904→40.8443561187 Å / SU ML: 0.0783588348951 / Cross valid method: FREE R-VALUE / σ(F): 1.33649116274 / Phase error: 13.1095824723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.134769670725 8593 4.98595831593 %
Rwork0.129225627388 163751 -
obs0.129509197469 172344 99.9860763019 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.2059493131 Å2
Refinement stepCycle: LAST / Resolution: 0.860002552904→40.8443561187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 20 218 1633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005917327096581517
X-RAY DIFFRACTIONf_angle_d0.9452304052142079
X-RAY DIFFRACTIONf_chiral_restr0.0646888183896237
X-RAY DIFFRACTIONf_plane_restr0.00950995085662279
X-RAY DIFFRACTIONf_dihedral_angle_d17.429674008585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.860002552904-0.86980.2950975533272900.2624582170135427X-RAY DIFFRACTION99.9300821535
0.8698-0.880.2469111757992730.2532516734595468X-RAY DIFFRACTION100
0.88-0.89070.2294996201392810.2348218219015428X-RAY DIFFRACTION99.9649798634
0.8907-0.9020.2189595613582830.2237021873675404X-RAY DIFFRACTION99.9648444366
0.902-0.91390.2095945244242720.2178421081025453X-RAY DIFFRACTION99.9825358016
0.9139-0.92640.1894408618542740.1986135385535450X-RAY DIFFRACTION99.9301675978
0.9264-0.93960.1910506410862750.1817622620815492X-RAY DIFFRACTION99.9653319466
0.9396-0.95370.2051621718542660.1779528552795411X-RAY DIFFRACTION99.9823881648
0.9537-0.96860.1639555490233090.1680755829925459X-RAY DIFFRACTION99.9653379549
0.9686-0.98450.1580612933282840.1585421393345402X-RAY DIFFRACTION100
0.9845-1.00140.1636377404842870.1524389182645432X-RAY DIFFRACTION99.9825174825
1.0014-1.01960.1536351012812890.1461565896555456X-RAY DIFFRACTION99.9825965889
1.0196-1.03930.1347704493062660.1352941523185459X-RAY DIFFRACTION99.9825358016
1.0393-1.06050.1391237037752620.1352288487965455X-RAY DIFFRACTION100
1.0605-1.08350.1344993885433020.1312857898065449X-RAY DIFFRACTION100
1.0835-1.10870.1283810592212880.1263920589855408X-RAY DIFFRACTION100
1.1087-1.13650.1257160352332940.1190483195195453X-RAY DIFFRACTION100
1.1365-1.16720.1288508239043120.1148190320175463X-RAY DIFFRACTION100
1.1672-1.20150.106450644812700.1170792594985434X-RAY DIFFRACTION100
1.2015-1.24030.09722157246512830.1209841422265471X-RAY DIFFRACTION100
1.2403-1.28470.1216487663582710.1186430336895471X-RAY DIFFRACTION100
1.2847-1.33610.1145881438972780.1169913359835477X-RAY DIFFRACTION100
1.3361-1.39690.1202257925152570.1197890515335485X-RAY DIFFRACTION100
1.3969-1.47060.1285796648322880.1159856040645460X-RAY DIFFRACTION100
1.4706-1.56270.1092643003563310.1089492499695416X-RAY DIFFRACTION100
1.5627-1.68340.127531910972750.1074240546545512X-RAY DIFFRACTION100
1.6834-1.85280.1121995202923030.1112366251575472X-RAY DIFFRACTION100
1.8528-2.12090.1078835132992750.106161860675512X-RAY DIFFRACTION100
2.1209-2.6720.1192650972443350.1111490480855467X-RAY DIFFRACTION100
2.672-40.84435611870.1584109258583200.1428418926515605X-RAY DIFFRACTION99.9662561161

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