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- PDB-7odx: Cyanophage S-2L Succinoaminodeoxyadenylate synthetase (PurZ) boun... -

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Basic information

Entry
Database: PDB / ID: 7odx
TitleCyanophage S-2L Succinoaminodeoxyadenylate synthetase (PurZ) bound to dGMP and dATP as an energy donor
ComponentsSuccinoaminodeoxyadenylate synthetase (PurZ)
KeywordsVIRAL PROTEIN / S-2L / Succinoaminodeoxyadenylate synthetase / PurZ
Function / homology2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Function and homology information
Biological speciesCyanophage S-2L (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69617086092 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinoaminodeoxyadenylate synthetase (PurZ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7363
Polymers39,8971
Non-polymers8382
Water7,098394
1
A: Succinoaminodeoxyadenylate synthetase (PurZ)
hetero molecules

A: Succinoaminodeoxyadenylate synthetase (PurZ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4716
Polymers79,7942
Non-polymers1,6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area8220 Å2
ΔGint-17 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.180, 108.180, 142.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-817-

HOH

21A-838-

HOH

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Components

#1: Protein Succinoaminodeoxyadenylate synthetase (PurZ)


Mass: 39897.113 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-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxyguanosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% v/v Tacsimate; 2% w/v PEG 3350; 100 mM HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 14, 2019 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.69617086092→44.5 Å / Num. obs: 54836 / % possible obs: 99.8 % / Redundancy: 39.6 % / Biso Wilson estimate: 28.6904003452 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.013 / Rrim(I) all: 0.082 / Net I/σ(I): 34.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 39.4 % / Rmerge(I) obs: 2.661 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3903 / CC1/2: 0.694 / Rpim(I) all: 0.419 / Rrim(I) all: 2.695 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FM1

6fm1


Resolution: 1.69617086092→44.4954227156 Å / SU ML: 0.258644893723 / Cross valid method: FREE R-VALUE / σ(F): 1.33794450571 / Phase error: 17.7125464286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.17601031371 2738 4.99990869414 %
Rwork0.159386977715 52023 -
obs0.160215360219 54761 99.7104879825 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.2959699757 Å2
Refinement stepCycle: LAST / Resolution: 1.69617086092→44.4954227156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 53 394 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009595542072832821
X-RAY DIFFRACTIONf_angle_d1.004368890563856
X-RAY DIFFRACTIONf_chiral_restr0.0678462690405431
X-RAY DIFFRACTIONf_plane_restr0.00535924337827530
X-RAY DIFFRACTIONf_dihedral_angle_d26.45795681021061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6962-1.72540.3981345575561290.4243336783142462X-RAY DIFFRACTION96.6791044776
1.7254-1.75680.4614288927911350.39715954312561X-RAY DIFFRACTION99.5568685377
1.7568-1.79060.3916394871611340.3429898577942548X-RAY DIFFRACTION99.7026022305
1.7906-1.82710.323829459331350.2706121337492562X-RAY DIFFRACTION99.667405765
1.8271-1.86690.2276862988221350.2207429998812561X-RAY DIFFRACTION99.8518518519
1.8669-1.91030.1829118020071340.188470254642549X-RAY DIFFRACTION99.6286669142
1.9103-1.95810.2219544129891360.1739875732232574X-RAY DIFFRACTION99.8526160648
1.9581-2.0110.1677604207071360.1673067547242581X-RAY DIFFRACTION99.8897058824
2.011-2.07020.1705219791191340.1735928611282553X-RAY DIFFRACTION99.8513563731
2.0702-2.1370.1850936948871360.1660561643042584X-RAY DIFFRACTION100
2.137-2.21340.1810900853141370.1514347317192596X-RAY DIFFRACTION99.9268738574
2.2134-2.3020.1875831623321360.1439759730052588X-RAY DIFFRACTION99.9266324285
2.302-2.40680.1911205281281370.1516780833792599X-RAY DIFFRACTION100
2.4068-2.53360.1733006666091370.1529072603942599X-RAY DIFFRACTION100
2.5336-2.69240.182525438121370.1557032695242605X-RAY DIFFRACTION100
2.6924-2.90020.1737993941681380.1577637192272624X-RAY DIFFRACTION99.9638074557
2.9002-3.1920.1689218737361390.1533431177582650X-RAY DIFFRACTION99.9641577061
3.192-3.65370.1463466961271400.137494848182657X-RAY DIFFRACTION100
3.6537-4.60250.1454933492331420.1267623647132703X-RAY DIFFRACTION99.9648629656
4.6025-44.49542271560.1592325229791510.1571579086212867X-RAY DIFFRACTION99.7026759167
Refinement TLS params.Method: refined / Origin x: -38.8667272725 Å / Origin y: 22.2396766755 Å / Origin z: 4.48387363243 Å
111213212223313233
T0.149412169561 Å2-0.00771247897798 Å2-0.0066770729049 Å2-0.212181028262 Å2-0.0114184993924 Å2--0.204513653481 Å2
L0.454222695706 °2-0.103249180312 °2-0.00448418941085 °2-0.481764405197 °2-0.13562387487 °2--1.21950126864 °2
S0.00505194620226 Å °-0.023595824819 Å °0.019088831861 Å °0.0373330694 Å °0.00709769341036 Å °-0.113682898502 Å °-0.016416008882 Å °0.184857715382 Å °-0.00774499303787 Å °
Refinement TLS groupSelection details: all

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