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- PDB-8qwa: Adenylosuccinate Synthetase from H. pylori in complex with PLP and IMP -

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Basic information

Entry
Database: PDB / ID: 8qwa
TitleAdenylosuccinate Synthetase from H. pylori in complex with PLP and IMP
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / purine salvage pathway / complex with inhibitor / AMP precursos synthesis
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBzowska, A. / Narczyk, M. / Maksymiuk, W.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreHarmonia 2015/18/M/NZ1/00776 Poland
Ministry of Science and Higher Education (Poland)IDUB PSP-501-D111-20-0004316 Poland
CitationJournal: J Enzyme Inhib Med Chem / Year: 2024
Title: Vitamin B6 inhibits activity of Helicobacter pylori adenylosuccinate synthetase and growth of reference and clinical, antibiotic-resistant H. pylori strains.
Authors: Wojtys, M.I. / Maksymiuk, W. / Narczyk, M. / Bubic, A. / Asler, I.L. / Krzyzek, P. / Gosciniak, G. / Jagusztyn-Krynicka, E.K. / Bzowska, A.
History
DepositionOct 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5935
Polymers45,8101
Non-polymers7844
Water4,756264
1
A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,18610
Polymers91,6192
Non-polymers1,5678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area8460 Å2
ΔGint-61 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.897, 61.124, 119.254
Angle α, β, γ (deg.)90.000, 98.905, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

21A-740-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenylosuccinate synthetase / AMPSase / AdSS / IMP--aspartate ligase


Mass: 45809.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: ATCC 700392 / 26695 / Gene: purA, HP_0255 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P56137, adenylosuccinate synthase

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 285 K / Method: counter-diffusion / pH: 8.5
Details: 85mM Tris-HCl pH 8,5 21% PEG4k 170 mM Li2SO4 15% GOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.54184 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.85→29.821 Å / Num. obs: 41958 / % possible obs: 100 % / Redundancy: 23.5 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Net I/σ(I): 48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.06-29.823.20.01637510.0040.017
1.85-1.8912.70.2425800.9910.1020.261

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→29.821 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.157 / SU B: 2.372 / SU ML: 0.072 / Average fsc free: 0.9728 / Average fsc work: 0.9827 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2011 4135 9.876 %
Rwork0.1669 37735 -
all0.17 --
obs-41870 99.752 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.066 Å20 Å20.738 Å2
2--0.14 Å20 Å2
3----0.291 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 49 264 3489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123294
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163178
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.8424449
X-RAY DIFFRACTIONr_angle_other_deg0.661.7817365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.865518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00810604
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.42110136
X-RAY DIFFRACTIONr_chiral_restr0.1050.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
X-RAY DIFFRACTIONr_nbd_refined0.2240.2635
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23038
X-RAY DIFFRACTIONr_nbtor_refined0.180.21619
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21710
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.220
X-RAY DIFFRACTIONr_nbd_other0.1880.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.227
X-RAY DIFFRACTIONr_mcbond_it1.9311.6891626
X-RAY DIFFRACTIONr_mcbond_other1.8921.6891626
X-RAY DIFFRACTIONr_mcangle_it2.7633.0292030
X-RAY DIFFRACTIONr_mcangle_other2.7633.0292031
X-RAY DIFFRACTIONr_scbond_it3.3922.1261668
X-RAY DIFFRACTIONr_scbond_other3.3912.1281669
X-RAY DIFFRACTIONr_scangle_it5.1993.6852417
X-RAY DIFFRACTIONr_scangle_other5.1983.6872418
X-RAY DIFFRACTIONr_lrange_it6.2617.1463738
X-RAY DIFFRACTIONr_lrange_other6.18616.8433679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.2623090.19527570.20230660.960.9781000.166
1.898-1.950.233000.18827050.19230050.9680.9791000.161
1.95-2.0060.2383070.1825990.18629060.9680.981000.155
2.006-2.0670.2212570.17225670.17728260.9710.98299.92920.151
2.067-2.1350.2162780.1824900.18427680.9710.9811000.159
2.135-2.2090.2132560.17424050.17826640.9730.98299.88740.154
2.209-2.2920.2262290.17423360.17925660.9710.98299.9610.156
2.292-2.3850.2342550.17121930.17724560.970.98299.67430.152
2.385-2.4910.2152230.16721380.17223750.970.98499.41050.148
2.491-2.6110.2182270.15720490.16322800.9740.98699.82460.142
2.611-2.7510.2242410.17419110.17921650.9720.98399.39950.157
2.751-2.9170.1821960.16918310.1720360.980.98399.5580.156
2.917-3.1160.2191680.1717680.17419450.9670.98299.53730.16
3.116-3.3630.1971800.16916130.17217990.9780.98499.66650.165
3.363-3.6790.1721520.16414990.16516550.9840.98599.75830.161
3.679-4.1050.1691550.14613490.14915140.9840.98899.33950.149
4.105-4.7250.1381610.12611810.12713450.990.99199.7770.131
4.725-5.7510.1771150.16910220.1711380.9870.98899.91210.175
5.751-7.9870.187660.178410.1719070.9820.9861000.175
7.987-29.8210.198600.1714810.1735450.9670.98399.26610.172

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