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

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Basic information

Entry
Database: PDB / ID: 6yvq
TitleCrystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in apo form
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
Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 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 28, 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)34,2796
Polymers33,9001
Non-polymers3785
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-18 kcal/mol
Surface area13530 Å2
Unit cell
Length a, b, c (Å)48.078, 64.287, 48.020
Angle α, β, γ (deg.)90.000, 110.550, 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-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiSO4, 0.1 M Bis-Tris pH 5.5, 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: 1.48→45.02 Å / Num. obs: 41027 / % possible obs: 89.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.49 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.04 / Rrim(I) all: 0.085 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.48-1.582.90.27747130.8920.1910.3457.4
4.18-45.024.30.05820750.9930.0320.06699.2

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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: 3R9R

3r9r


Resolution: 1.48→45.018 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.1968 1975 4.82 %
Rwork0.162 --
obs0.1637 40998 89.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.85 Å2 / Biso mean: 22.7098 Å2 / Biso min: 10.7 Å2
Refinement stepCycle: final / Resolution: 1.48→45.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 22 280 2550
Biso mean--28.76 32.98 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062350
X-RAY DIFFRACTIONf_angle_d1.0453213
X-RAY DIFFRACTIONf_chiral_restr0.042358
X-RAY DIFFRACTIONf_plane_restr0.005424
X-RAY DIFFRACTIONf_dihedral_angle_d11.26844
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.48-1.51570.2612950.2286154350
1.5157-1.55670.2298830.2084181058
1.5567-1.60250.23541040.201216069
1.6025-1.65420.23351230.1843264285
1.6542-1.71330.21181500.182304998
1.7133-1.78190.211570.1735304499
1.7819-1.8630.19571560.1715306299
1.863-1.96120.2061680.1725308499
1.9612-2.08410.22131350.1639309399
2.0841-2.2450.19191950.1615302099
2.245-2.47090.19021650.16613109100
2.4709-2.82850.22591170.1728316699
2.8285-3.56330.18951550.1619308299
3.5633-45.0180.1741720.1357315999
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)
12.36671.19571.60081.59660.48411.72380.1954-0.0199-0.30670.1139-0.035-0.17850.16130.0775-0.13490.1799-0.0038-0.00430.17130.02290.148138.6708-13.155864.7624
21.84660.2999-0.34930.36830.03480.3225-0.04080.0104-0.0381-0.0410.02020.02370.0095-0.01020.01760.132-0.0008-0.01240.13520.01280.130546.9811-3.707753.0229
30.82560.41750.34211.4861.06771.48530.0433-0.0334-0.03330.0013-0.0375-0.00460.0361-0.0657-0.00160.1254-0.00060.00270.11830.01340.129150.7413-2.649349.8115
42.8139-0.31881.32041.9545-0.66142.87380.0609-0.0874-0.0560.2658-0.103-0.0883-0.15480.24030.06670.1872-0.05520.02150.1703-0.00340.134849.02231.534971.6705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 137 )A49 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 240 )A138 - 240
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 295 )A241 - 295

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