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- PDB-6yx3: Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 6yx3
TitleCrystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in complex with ATP
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 / cytoplasm
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
ADENOSINE-5'-TRIPHOSPHATE / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 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
DepositionApr 30, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7206
Polymers33,9001
Non-polymers8205
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-54 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.758, 64.114, 49.013
Angle α, β, γ (deg.)90.000, 111.480, 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)
Gene: purC, MAB_0689 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MHW4, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 40.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiSO4, 0.1 M Bis-Tris pH 6.0, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.22→45.61 Å / Num. obs: 62449 / % possible obs: 76.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 9.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rrim(I) all: 0.049 / Net I/σ(I): 23.1 / Num. measured all: 302987
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
1.22-1.292.60.342619523410.8080.2470.4243.317.8
3.66-45.615.10.0331519229950.9970.0160.03742.696.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
Aimless0.5.1data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVQ

6yvq


Resolution: 1.22→37.165 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1792 3066 4.91 %
Rwork0.1614 59352 -
obs0.1623 62418 76.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.28 Å2 / Biso mean: 16.8884 Å2 / Biso min: 5.59 Å2
Refinement stepCycle: final / Resolution: 1.22→37.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 47 406 2728
Biso mean--30.01 28.2 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062402
X-RAY DIFFRACTIONf_angle_d1.1143295
X-RAY DIFFRACTIONf_chiral_restr0.043364
X-RAY DIFFRACTIONf_plane_restr0.005427
X-RAY DIFFRACTIONf_dihedral_angle_d13.612866
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.22-1.23880.5882180.40182638
1.2388-1.25920.2552290.259753115
1.2592-1.28090.2276390.232381623
1.2809-1.30420.2723550.213113532
1.3042-1.32920.2029920.1913143241
1.3292-1.35640.1893740.1861180251
1.3564-1.38590.22011010.1839220563
1.3859-1.41810.21041400.1802256473
1.4181-1.45360.21331660.1741302185
1.4536-1.49290.19311910.1701324494
1.4929-1.53680.16642090.1723349399
1.5368-1.58640.18191730.16953510100
1.5864-1.64310.23671580.16563565100
1.6431-1.70890.18351900.16963508100
1.7089-1.78670.1841530.17293539100
1.7867-1.88090.21471640.16933570100
1.8809-1.99870.17621990.16213511100
1.9987-2.1530.18531650.15263546100
2.153-2.36960.17291590.15513576100
2.3696-2.71240.17521880.1613352399
2.7124-3.4170.18291940.156353799
3.417-37.1650.14282090.1437346197
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29780.24940.07533.5178-1.40352.80420.0928-0.15160.27410.16780.05510.0645-0.29060.044-0.1250.0966-0.00990.0060.0898-0.02350.097644.410815.194852.8602
20.53410.1232-0.54510.0698-0.15880.72820.0239-0.01280.0313-0.00210.00110.004-0.04390.0406-0.03220.07470.0021-0.00510.0831-0.00590.081637.2474.749662.1475
30.8976-0.37570.13580.7463-0.23770.84760.00490.00520.0327-0.0052-0.0199-0.0041-0.01630.03130.00420.0549-0.008-0.00460.0604-0.00340.075626.04371.046267.7344
40.6580.29560.59011.17990.65262.00390.0756-0.0824-0.02420.0903-0.0076-0.02370.0194-0.0155-0.0760.0615-0.00560.02460.10360.01140.08847.6024-2.05872.0037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 31 )A0 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 117 )A32 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 240 )A118 - 240
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 296 )A241 - 296

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