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- PDB-6yy8: Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 6yy8
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-Q0N / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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)34,5166
Polymers33,9001
Non-polymers6165
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-22 kcal/mol
Surface area13370 Å2
Unit cell
Length a, b, c (Å)47.787, 64.771, 48.311
Angle α, β, γ (deg.)90.000, 110.800, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-Q0N / 4-azanyl-6-[1-(2-morpholin-4-ylethyl)pyrazol-4-yl]pyrimidine-5-carbonitrile


Mass: 299.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N7O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
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: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.3→37.05 Å / Num. obs: 67509 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 13.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 21 / Num. measured all: 375855
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
1.3-1.374.20.2674038597220.9470.1470.3063.999
4.11-37.055.90.0291313122120.9990.0130.0325599.8

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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: 1.3→37.047 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.52
RfactorNum. reflection% reflection
Rfree0.1802 3294 4.88 %
Rwork0.153 --
obs0.1543 67476 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.54 Å2 / Biso mean: 18.6798 Å2 / Biso min: 7.9 Å2
Refinement stepCycle: final / Resolution: 1.3→37.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 40 338 2634
Biso mean--30.96 30.44 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062385
X-RAY DIFFRACTIONf_angle_d1.0493266
X-RAY DIFFRACTIONf_chiral_restr0.04362
X-RAY DIFFRACTIONf_plane_restr0.005430
X-RAY DIFFRACTIONf_dihedral_angle_d13.374859
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.31840.24821250.216262799
1.3184-1.33810.19291350.1884261398
1.3381-1.3590.22271280.1751265599
1.359-1.38130.19411290.17142691100
1.3813-1.40510.19711550.15752646100
1.4051-1.43070.17411450.15872656100
1.4307-1.45820.17921390.15532667100
1.4582-1.48790.19961310.14222685100
1.4879-1.52030.19631560.14522648100
1.5203-1.55570.18181480.14992659100
1.5557-1.59460.17631390.14262656100
1.5946-1.63770.20421530.14422642100
1.6377-1.68590.18121240.1462706100
1.6859-1.74030.17691290.14892680100
1.7403-1.80250.18941300.14732688100
1.8025-1.87460.16821150.15112698100
1.8746-1.960.18741540.14612667100
1.96-2.06330.17431430.14132680100
2.0633-2.19250.16611350.14312691100
2.1925-2.36180.17121330.14832679100
2.3618-2.59940.18221400.16132697100
2.5994-2.97540.1971400.16762687100
2.9754-3.74820.17031260.15812709100
3.7482-37.0470.1691420.14672755100

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