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- PDB-6fm1: Deoxyguanylosuccinate synthase (DgsS) quaternary structure with A... -

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Basic information

Entry
Database: PDB / ID: 6fm1
TitleDeoxyguanylosuccinate synthase (DgsS) quaternary structure with ATPanddGMP at 2.3 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
ADENOSINE-5'-TRIPHOSPHATE / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / N6-succino-2-amino-2'-deoxyadenylate synthase
Similarity search - Component
Biological speciesVibrio phage phiVC8 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.35 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 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,03914
Polymers80,7862
Non-polymers2,25312
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-72 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.260, 90.260, 188.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenylosuccinate synthetase / Adenylosuccinate synthase


Mass: 40393.062 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 546 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxyguanosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.5 M KCl 10 %w/v Glycerol 12 %w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.3→47 Å / Num. obs: 35274 / % possible obs: 99.7 % / Redundancy: 13.6 % / Biso Wilson estimate: 45.55 Å2 / Net I/σ(I): 12.58
Reflection shellResolution: 2.3→2.44 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.35→30.97 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.477 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1618 5 %RANDOM
Rwork0.183 ---
obs0.185 32353 97.3 %-
Displacement parametersBiso mean: 30.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.1046 Å20 Å20 Å2
2---2.1046 Å20 Å2
3---4.2093 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.35→30.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5301 0 141 534 5976
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015552HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.177543HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1922SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes141HARMONIC2
X-RAY DIFFRACTIONt_gen_planes848HARMONIC5
X-RAY DIFFRACTIONt_it5552HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion16.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion724SEMIHARMONIC5
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_contact8263SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.43 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.342 144 5 %
Rwork0.2638 2734 -
all0.2676 2878 -
obs--95.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5718-0.09530.10210.51680.14481.0508-0.0191-0.0050.0896-0.0052-0.03130.0005-0.1902-0.02940.0504-0.03030.0133-0.0097-0.0815-0.0113-0.0941-42.710915.18462.1568
20.36960.1013-0.12460.45190.25340.6614-0.019-0.0266-0.04030.0516-0.03090.01690.11090.05330.05-0.04980.01530.0011-0.0416-0.0042-0.087-36.4098-13.50357.2402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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