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- PDB-6flf: Deoxyguanylosuccinate synthase (DgsS) structure at 1.33 Angstrom ... -

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Basic information

Entry
Database: PDB / ID: 6flf
TitleDeoxyguanylosuccinate synthase (DgsS) structure at 1.33 Angstrom resolution.
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsBIOSYNTHETIC PROTEIN / 2 / 6-diaminopurine / phage phiVC8 / Synthetase
Function / homology
Function and homology information


2-amino-2'-deoxyadenylo-succinate synthase / adenylosuccinate synthase activity / purine nucleotide biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
N6-succino-2-amino-2'-deoxyadenylate synthase / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
N6-succino-2-amino-2'-deoxyadenylate synthase
Similarity search - Component
Biological speciesVibrio phage phiVC8 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsSleiman, D. / Loc'h, J. / Haouz, A. / Kaminski, P.A.
CitationJournal: Science / Year: 2021
Title: A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes.
Authors: Sleiman, D. / Garcia, P.S. / Lagune, M. / Loc'h, J. / Haouz, A. / Taib, N. / Rothlisberger, P. / Gribaldo, S. / Marliere, P. / Kaminski, P.A.
History
DepositionJan 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate synthetase


Theoretical massNumber of molelcules
Total (without water)40,3931
Polymers40,3931
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.920, 59.480, 73.980
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-542-

HOH

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Components

#1: Protein Adenylosuccinate synthetase / Adenylosuccinate synthase / Deoxyguanylosuccinate synthase


Mass: 40392.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage phiVC8 (virus) / Gene: phiVC8_p27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3FFN6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2M NaCl 12% PEG 6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.33→49.4 Å / Num. obs: 88372 / % possible obs: 99.2 % / Redundancy: 4.74 % / Biso Wilson estimate: 23.56 Å2 / Net I/σ(I): 8.4
Reflection shellResolution: 1.33→1.41 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→49.4 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.053
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4407 5 %RANDOM
Rwork0.2 ---
obs0.201 88135 99.8 %-
Displacement parametersBiso mean: 29.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.6206 Å20 Å20.2082 Å2
2---2.9454 Å20 Å2
3---0.3247 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.33→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 0 350 2725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012430HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043291HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d840SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes351HARMONIC5
X-RAY DIFFRACTIONt_it2430HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion14.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion315SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3129SEMIHARMONIC4
LS refinement shellResolution: 1.33→1.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 323 4.99 %
Rwork0.3485 6150 -
all0.3491 6473 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 3.6476 Å / Origin y: 15.1999 Å / Origin z: 14.1167 Å
111213212223313233
T-0.0175 Å2-0.0144 Å20.0076 Å2--0.0355 Å2-0.0153 Å2---0.0699 Å2
L0.8768 °20.3214 °2-0.0202 °2-0.5337 °2-0.0385 °2--0.7726 °2
S0.0611 Å °-0.1763 Å °0.0867 Å °0.1124 Å °-0.0656 Å °-0.0184 Å °-0.0118 Å °0.0246 Å °0.0045 Å °
Refinement TLS groupSelection details: { A|* }

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