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- PDB-6fm3: Deoxyguanylosuccinate synthase (DgsS) structure with ADP at 1.9 A... -

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Basic information

Entry
Database: PDB / ID: 6fm3
TitleDeoxyguanylosuccinate synthase (DgsS) structure with ADP at 1.9 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'-DIPHOSPHATE / N6-succino-2-amino-2'-deoxyadenylate synthase
Similarity search - Component
Biological speciesVibrio phage phiVC8 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsSleiman, D. / Loc'h, J. / Haouz, A. / Kaminski, P.A.
CitationJournal: To Be Published
Title: Deoxyguanylosuccinate synthase (DgsS) quaternary structure with ATP0, dGMP, Magnesium at 2.3 Angstrom resolution
Authors: Sleiman, D. / Loc'h, J. / Haouz, A. / Kaminski, P.A.
History
DepositionJan 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 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: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8563
Polymers40,3931
Non-polymers4632
Water6,431357
1
A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7116
Polymers80,7862
Non-polymers9254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6220 Å2
ΔGint-62 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.780, 58.200, 71.960
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Adenylosuccinate synthetase / Adenylosuccinate 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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 2M NaCl 12%w/v PEG 6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.9→48.32 Å / Num. obs: 24769 / % possible obs: 93.7 % / Redundancy: 5.59 % / Biso Wilson estimate: 41.98 Å2 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.44 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.95→48.32 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1238 5 %RANDOM
Rwork0.22 ---
obs0.222 24754 94.1 %-
Displacement parametersBiso mean: 36.62 Å2
Baniso -1Baniso -2Baniso -3
1-3.9786 Å20 Å2-1.0621 Å2
2---7.9768 Å20 Å2
3---3.9983 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 1.95→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 28 357 2742
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092434HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153304HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d833SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes363HARMONIC5
X-RAY DIFFRACTIONt_it2434HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion16.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion318SEMIHARMONIC5
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_contact3893SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.04 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.7427 141 4.99 %
Rwork0.5627 2686 -
all0.5713 2827 -
obs--88.19 %
Refinement TLS params.Method: refined / Origin x: -11.3624 Å / Origin y: -11.4532 Å / Origin z: 21.3026 Å
111213212223313233
T-0.0531 Å20.0089 Å2-0.0055 Å2--0.1326 Å20.0178 Å2---0.0061 Å2
L1.0978 °2-0.2266 °2-0.1797 °2-0.3713 °20.1481 °2--1.0633 °2
S0.0183 Å °0.1427 Å °0.0834 Å °-0.0264 Å °-0.0281 Å °-0.0148 Å °-0.0444 Å °-0.0596 Å °0.0098 Å °
Refinement TLS groupSelection details: { A|* }

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