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- PDB-6z0r: Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 6z0r
TitleCrystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in complex with fragment 1
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
4-azanylpyrimidine-5-carbonitrile / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesMycobacteroides abscessus ATCC 19977 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.308 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 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 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)34,2405
Polymers33,9001
Non-polymers3404
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-8 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.493, 64.729, 48.238
Angle α, β, γ (deg.)90.000, 110.880, 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 ATCC 19977 (bacteria)
Gene: purC, MAB_0689 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MHW4, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical ChemComp-Q4H / 4-azanylpyrimidine-5-carbonitrile


Mass: 120.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiSO4, 0.1 M Bis-Tris pH 5.5, 20 % 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: 1.308→45.07 Å / Num. obs: 60958 / % possible obs: 92.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 15.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 15.6
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
1.31-1.383.80.4752357361590.8240.2690.5492.364.9
4.14-45.076.10.0421314721510.9980.0180.04538.199.6

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.5.7phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVQ

6yvq


Resolution: 1.308→45.07 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 3034 4.98 %
Rwork0.1798 57902 -
obs0.1808 60936 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.33 Å2 / Biso mean: 21.3575 Å2 / Biso min: 10.51 Å2
Refinement stepCycle: final / Resolution: 1.308→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 22 306 2572
Biso mean--21.36 30.02 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062366
X-RAY DIFFRACTIONf_angle_d1.0353240
X-RAY DIFFRACTIONf_chiral_restr0.042361
X-RAY DIFFRACTIONf_plane_restr0.006429
X-RAY DIFFRACTIONf_dihedral_angle_d12.026853
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.308-1.32830.3027900.2681161357
1.3283-1.350.30371070.2528179163
1.35-1.37330.23471080.2438195970
1.3733-1.39830.28991260.231215076
1.3983-1.42520.21151100.227235483
1.4252-1.45430.22591470.2157258391
1.4543-1.48590.2191380.1958276597
1.4859-1.52050.24171370.18972829100
1.5205-1.55850.22041450.19062829100
1.5585-1.60060.20221440.19162841100
1.6006-1.64780.22531300.18942854100
1.6478-1.70090.23761760.19252816100
1.7009-1.76170.21341670.19272817100
1.7617-1.83230.22611730.18872819100
1.8323-1.91570.21441370.18232846100
1.9157-2.01670.19761590.17722840100
2.0167-2.1430.20441230.16812839100
2.143-2.30850.18211490.17232846100
2.3085-2.54080.17741460.18382858100
2.5408-2.90840.22431470.19062846100
2.9084-3.6640.17871440.17632885100
3.664-45.070.18451310.15562922100

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