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

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Basic information

Entry
Database: PDB / ID: 6tnh
TitleDeoxyguanylosuccinate synthase (DgsS) quaternary structure with AMPPcP, dGMP, Asp, Magnesium at 2.21 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ASPARTIC ACID / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / N6-succino-2-amino-2'-deoxyadenylate synthase
Similarity search - Component
Biological speciesVibrio phage phiVC8 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
DepositionDec 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,53713
Polymers81,1952
Non-polymers2,34311
Water7,116395
1
A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9678
Polymers40,5971
Non-polymers1,3707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5705
Polymers40,5971
Non-polymers9734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.640, 91.640, 189.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 40597.270 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 (E. coli) / References: UniProt: G3FFN6

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Non-polymers , 6 types, 406 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1M LiSO4, 2%PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979346 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979346 Å / Relative weight: 1
ReflectionResolution: 2.21→47.38 Å / Num. obs: 40942 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 51.14 Å2 / CC1/2: 0.96 / Net I/σ(I): 6.88
Reflection shellResolution: 2.21→2.34 Å / Num. unique obs: 6300 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FLF

6flf


Resolution: 2.21→47.38 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.271 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2043 5 %RANDOM
Rwork0.192 ---
obs0.194 40865 99 %-
Displacement parametersBiso max: 148.74 Å2 / Biso mean: 52.91 Å2 / Biso min: 28.56 Å2
Baniso -1Baniso -2Baniso -3
1--7.3247 Å20 Å20 Å2
2---7.3247 Å20 Å2
3---14.6494 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.21→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 143 395 5861
Biso mean--66.9 51.72 -
Num. residues----689
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1921SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes853HARMONIC5
X-RAY DIFFRACTIONt_it5579HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion727SEMIHARMONIC5
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_contact7528SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5579HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg7589HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion15.58
LS refinement shellResolution: 2.21→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2467 145 5 %
Rwork0.2715 2753 -
all0.2702 2898 -
obs--96.65 %
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)
10.3085-0.0391-0.10060.44640.34870.6732-0.02610.0296-0.01830.065-0.03910.0350.06430.00130.06520.0336-0.00060.00390.0374-0.0077-0.13678.639232.23687.3342
20.3262-0.07130.03750.22150.18871.2224-0.0091-0.01290.0201-0.0488-0.0348-0.0099-0.1362-0.06450.04380.1120.0231-0.038-0.0294-0.0116-0.15252.327661.09912.4107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 343
2X-RAY DIFFRACTION2{ B|* }B0 - 343

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