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- PDB-6yya: Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 6yya
TitleCrystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in complex with inhibitor
ComponentsPhosphoribosylaminoimidazole-succinocarboxamide synthase
KeywordsLIGASE / SAICAR synthetase / Phosphoribosylaminoimidazole-succinocarboxamide synthase / PurC / Purine Biosynthesis
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / 'de novo' IMP biosynthetic process / ATP binding
Similarity search - Function
Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase
Similarity search - Domain/homology
Chem-PZK / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å
AuthorsThomas, S.E. / Charoensutthivarakul, S. / Coyne, A.G. / Abell, C. / Blundell, T.L.
Funding support Switzerland, United Kingdom, 2items
OrganizationGrant numberCountry
Other privateFondation Botnar Grant No.6063 Switzerland
Other privateCystic Fibrosis Trust SRC010 United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach.
Authors: Charoensutthivarakul, S. / Thomas, S.E. / Curran, A. / Brown, K.P. / Belardinelli, J.M. / Whitehouse, A.J. / Acebron-Garcia-de-Eulate, M. / Sangan, J. / Gramani, S.G. / Jackson, M. / Mendes, ...Authors: Charoensutthivarakul, S. / Thomas, S.E. / Curran, A. / Brown, K.P. / Belardinelli, J.M. / Whitehouse, A.J. / Acebron-Garcia-de-Eulate, M. / Sangan, J. / Gramani, S.G. / Jackson, M. / Mendes, V. / Floto, R.A. / Blundell, T.L. / Coyne, A.G. / Abell, C.
History
DepositionMay 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5737
Polymers33,9001
Non-polymers6736
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-27 kcal/mol
Surface area13390 Å2
Unit cell
Length a, b, c (Å)47.801, 64.956, 48.277
Angle α, β, γ (deg.)90.000, 110.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase


Mass: 33900.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: purC, MAB_0689 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MHW4, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical ChemComp-PZK / 4-azanyl-6-[1-[(3-fluorophenyl)methyl]pyrazol-4-yl]pyrimidine-5-carbonitrile


Mass: 294.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11FN6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiSO4, 0.1 M Bis-Tris pH 6.0, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.409→39.544 Å / Num. obs: 53053 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.41-1.484.70.2543504374740.9750.1260.2856.296.4
4.45-39.545.50.06959717310.9950.0270.06627.499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 1

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVQ

6yvq


Resolution: 1.41→39.54 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.01
RfactorNum. reflection% reflection
Rfree0.2152 2701 5.09 %
Rwork0.1864 --
obs0.1879 53018 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.78 Å2 / Biso mean: 21.6569 Å2 / Biso min: 9.91 Å2
Refinement stepCycle: final / Resolution: 1.41→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 44 250 2542
Biso mean--22.34 30.29 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062382
X-RAY DIFFRACTIONf_angle_d1.1073257
X-RAY DIFFRACTIONf_chiral_restr0.042359
X-RAY DIFFRACTIONf_plane_restr0.006428
X-RAY DIFFRACTIONf_dihedral_angle_d12.078850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.41-1.43410.23671260.2503239190
1.4341-1.46170.27371260.22252664100
1.4617-1.49150.24481150.18842675100
1.4915-1.5240.19611320.19552652100
1.524-1.55940.21451680.19292647100
1.5594-1.59840.22751610.19312624100
1.5984-1.64160.26661180.1932673100
1.6416-1.690.21631350.19572659100
1.69-1.74450.22491410.19442661100
1.7445-1.80680.23671370.19352674100
1.8068-1.87920.2241210.19532673100
1.8792-1.96470.22741510.18792656100
1.9647-2.06830.22191520.18112663100
2.0683-2.19790.19091540.18632651100
2.1979-2.36750.20351530.18772635100
2.3675-2.60580.23521440.19922680100
2.6058-2.98270.22871600.19952655100
2.9827-3.75740.20991710.17982647100
3.7574-39.540.19461360.1678273799

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