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- PDB-6zxq: Adenylosuccinate Synthetase from H. pylori in complex with HDA, G... -

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Basic information

Entry
Database: PDB / ID: 6zxq
TitleAdenylosuccinate Synthetase from H. pylori in complex with HDA, GDP, IMO, Mg
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsLIGASE / Complex / Synthetase / N-C Ligase / Purine salvage pathway
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
GUANOSINE-5'-DIPHOSPHATE / HADACIDIN / 6-O-PHOSPHORYL INOSINE MONOPHOSPHATE / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBubic, A. / Stefanic, Z.
Funding support Croatia, 1items
OrganizationGrant numberCountry
Croatian Science Foundation Croatia
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site
Authors: Bubic, A. / Narczyk, M. / Petek, A. / Wojtys, M.I. / Maksymiuk, W. / Wielgus-Kutrowska, B. / Winiewska-Szajewska, M. / Pavkov-Keller, T. / Bertosa, B. / Stefanic, Z. / Luic, M. / Bzowska, A. / Lescic Asler, I.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)47,8965
Polymers46,8811
Non-polymers1,0154
Water8,179454
1
A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,79110
Polymers93,7622
Non-polymers2,0308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8760 Å2
ΔGint-67 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.706, 68.362, 68.828
Angle α, β, γ (deg.)90.000, 121.110, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-943-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 46880.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: purA, HP_0255 / Plasmid: pET21b(+) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): BL-21(DE3) RIL / References: UniProt: P56137, adenylosuccinate synthase

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Non-polymers , 5 types, 458 molecules

#2: Chemical ChemComp-HDA / HADACIDIN / Hadacidin


Mass: 119.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticancer, medication*YM
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-IMO / 6-O-PHOSPHORYL INOSINE MONOPHOSPHATE


Mass: 428.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O11P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulfate, Tris , PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033195 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033195 Å / Relative weight: 1
ReflectionResolution: 1.4→48.46 Å / Num. obs: 93653 / % possible obs: 98.5 % / Redundancy: 6.58 % / Biso Wilson estimate: 23.066 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.145 / Χ2: 0.972 / Net I/σ(I): 8.09 / Num. measured all: 616201
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.486.5261.3941.29565815271146590.3921.51396
1.48-1.586.3590.9981.848991614395141390.5231.08898.2
1.58-1.716.530.6593.268603313363131760.8370.71898.6
1.71-1.876.4760.3536.097940112369122600.9530.38499.1
1.87-2.096.8310.2199.577577611182110930.980.23799.2
2.09-2.426.5520.13113.1864563990498540.9880.14299.5
2.42-2.967.0170.0917.1258400834683230.9940.09899.7
2.96-4.186.6170.07420.842966652564930.9940.08199.5
4.18-48.466.4250.08122.623488369636560.990.08898.9

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Processing

Software
NameVersionClassification
PHENIXv1.17refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r7t

3r7t


Resolution: 1.4→48.46 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 2098 2.24 %
Rwork0.1512 91470 -
obs0.1521 93568 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.75 Å2 / Biso mean: 26.3089 Å2 / Biso min: 11.48 Å2
Refinement stepCycle: final / Resolution: 1.4→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 64 454 3702
Biso mean--16.03 40.52 -
Num. residues----410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.430.38881330.31155843597696
1.43-1.470.29491390.26446021616098
1.47-1.510.34651390.26856074621399
1.51-1.550.27421380.2466043618199
1.55-1.60.36051390.30126025616498
1.6-1.660.29321390.25256066620599
1.66-1.720.25951400.18676102624299
1.72-1.80.19651400.13716102624299
1.8-1.90.18281400.130761236263100
1.9-2.020.16471400.14526104624499
2.02-2.170.16821410.115861476288100
2.17-2.390.17351410.126961456286100
2.39-2.740.16681420.128761786320100
2.74-3.450.18271420.141862146356100
3.45-48.460.16411450.133762836428100

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