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- PDB-6wsi: Intact cis-2,3-epoxysuccinic acid bound to Isocitrate Lyase-1 fro... -

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Basic information

Entry
Database: PDB / ID: 6wsi
TitleIntact cis-2,3-epoxysuccinic acid bound to Isocitrate Lyase-1 from Mycobacterium tuberculosis
ComponentsIsocitrate lyase
KeywordsLYASE / enzyme / covalent inhibitor / substrate analog / Structural Genomics / PSI-Biology / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / DI(HYDROXYETHYL)ETHER / (2R,3S)-oxirane-2,3-dicarboxylic acid / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å
AuthorsKrieger, I.V. / Mellott, D. / Meek, T.D. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01A1095208 United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Covalent Inactivation of Mycobacterium tuberculosis Isocitrate Lyase by cis -2,3-Epoxy-Succinic Acid.
Authors: Pham, T.V. / Mellott, D.M. / Moghadamchargari, Z. / Chen, K. / Krieger, I. / Laganowsky, A. / Sacchettini, J.C. / Meek, T.D.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: 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 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate lyase
B: Isocitrate lyase
C: Isocitrate lyase
D: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,28438
Polymers188,5384
Non-polymers2,74734
Water21,1861176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39290 Å2
ΔGint-193 kcal/mol
Surface area48910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.170, 134.205, 161.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isocitrate lyase


Mass: 47134.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: aceA_1, aceA, aceA_2, icl1, DSI38_20225, E5M05_01375, ERS007661_00054, ERS007670_00334, ERS007681_01797, ERS007688_01303, ERS007703_00218, ERS007720_01262, ERS007722_00697, ERS007741_02575, ...Gene: aceA_1, aceA, aceA_2, icl1, DSI38_20225, E5M05_01375, ERS007661_00054, ERS007670_00334, ERS007681_01797, ERS007688_01303, ERS007703_00218, ERS007720_01262, ERS007722_00697, ERS007741_02575, ERS013471_01927, ERS023446_00716, ERS024276_00897, ERS027646_00855, ERS027659_01610, ERS027661_00891, ERS075361_01798, ERS094182_00218, F6W99_03123, FRD82_04680, SAMEA2683035_00941
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045H6H0, isocitrate lyase

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Non-polymers , 6 types, 1210 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H2O3
#4: Chemical
ChemComp-U9S / (2R,3S)-oxirane-2,3-dicarboxylic acid / cis-2,3-epoxysuccinic acid


Mass: 132.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1176 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 0.2 M NaAc, 25% PEG 4,000

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.749→71.048 Å / Num. obs: 172875 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rrim(I) all: 0.107 / Net I/σ(I): 10.1
Reflection shellResolution: 1.75→1.8 Å / Rmerge(I) obs: 1.008 / Mean I/σ(I) obs: 1 / Num. unique obs: 12489 / CC1/2: 0.544

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8I

1f8i


Resolution: 1.749→71.048 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 8534 4.94 %
Rwork0.1635 164095 -
obs0.1651 172629 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.84 Å2 / Biso mean: 24.0292 Å2 / Biso min: 12.3 Å2
Refinement stepCycle: final / Resolution: 1.749→71.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13232 0 170 1176 14578
Biso mean--29.56 29.02 -
Num. residues----1708
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.749-1.76840.34882800.3281495092
1.7684-1.78920.32152830.2907540099
1.7892-1.8110.2922930.27145387100
1.811-1.8340.29233050.25475424100
1.834-1.85810.29472780.24485381100
1.8581-1.88350.25253000.21845454100
1.8835-1.91050.25612920.20765391100
1.9105-1.9390.24772780.19465469100
1.939-1.96930.22342610.19145463100
1.9693-2.00160.23392930.18655426100
2.0016-2.03610.22942920.18815476100
2.0361-2.07310.23062640.18175437100
2.0731-2.1130.23072940.18075430100
2.113-2.15610.21582630.17675474100
2.1561-2.2030.20943050.16585430100
2.203-2.25420.21352810.16565481100
2.2542-2.31060.2082770.16425463100
2.3106-2.37310.21972930.16045454100
2.3731-2.44290.17842760.16375469100
2.4429-2.52180.21132720.1625509100
2.5218-2.61190.21053100.16365432100
2.6119-2.71650.20122830.16075518100
2.7165-2.84010.17162800.1595512100
2.8401-2.98990.17562850.15495525100
2.9899-3.17720.18022670.16235534100
3.1772-3.42250.1863080.15655506100
3.4225-3.76690.15962570.14075613100
3.7669-4.31190.15372620.12795609100
4.3119-5.43230.14883060.12755614100
5.4323-71.0480.17182960.15285864100

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