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- PDB-6vb9: Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lya... -

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Basic information

Entry
Database: PDB / ID: 6vb9
TitleCovalent adduct of cis-2,3-epoxysuccinic acid with 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 / methylisocitrate lyase activity / isocitrate lyase activity / isocitrate metabolic process / glyoxylate cycle / zymogen binding / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region / metal ion binding ...isocitrate lyase / methylisocitrate lyase activity / isocitrate lyase activity / isocitrate metabolic process / glyoxylate cycle / zymogen binding / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / OXALIC ACID / DI(HYDROXYETHYL)ETHER / Isocitrate lyase / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 Å
AuthorsKrieger, I.V. / Pham, T.V. / 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
DepositionDec 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Mar 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 1.3Oct 11, 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

Downloads & links

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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)191,47826
Polymers190,1954
Non-polymers1,28322
Water17,493971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34410 Å2
ΔGint-209 kcal/mol
Surface area49110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.065, 129.065, 167.825
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: 47548.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Cys 196 is chemically modified by cis-2,3-epoxysuccinic acid
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: aceA_1, aceA, ERS007703_00218, ERS023446_00716, ERS027651_01707, EZX46_15490, FDK60_05445, FDK62_09180, SAMEA2682864_01056, SAMEA2683035_00941
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045H6H0, UniProt: P9WKK7*PLUS, isocitrate lyase

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Non-polymers , 5 types, 993 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H2O4
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsGOX represents glyoxylate hydrate

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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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.0 Sodium Acetate (0.2 M) 30% PEG 4000

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Data collection

DiffractionMean temperature: 160 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 120374 / % possible obs: 90.7 % / Redundancy: 9 % / Biso Wilson estimate: 24.56 Å2 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.104 / Rrim(I) all: 0.318 / Χ2: 0.559 / Net I/σ(I): 2.2 / Num. measured all: 1087767
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.914.92.68734940.1311.33.0020.44153.1
1.91-1.955.32.40338820.1961.1172.6620.44859.4
1.95-1.985.62.10143410.280.9382.3110.45666.1
1.98-2.036.11.92647710.3110.8262.1030.45172.5
2.03-2.076.61.65551990.3860.6841.7980.46279.3
2.07-2.127.11.44457680.460.5741.5590.46987.7
2.12-2.177.91.27362420.550.4791.3650.47595.3
2.17-2.239.81.1466170.7120.3831.2050.47999.8
2.23-2.2910.41.02865980.7490.3361.0830.499100
2.29-2.3710.30.87865520.8330.2880.9250.501100
2.37-2.4510.20.76365870.8570.2520.8040.513100
2.45-2.559.60.63566280.8640.2170.6730.51999.8
2.55-2.6710.20.51366130.9220.1690.5410.53799.9
2.67-2.8110.40.43466300.9470.1420.4580.54599.9
2.81-2.9810.10.33466530.9660.1110.3530.592100
2.98-3.219.70.27266040.970.0920.2880.62999.3
3.21-3.5410.40.19866780.9850.0640.2080.68100
3.54-4.05100.1467050.9910.0460.1470.74899.9
4.05-5.110.20.1167930.9940.0360.1160.70999.8
5.1-509.60.08570190.9970.0290.090.59799.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8I

1f8i


Resolution: 1.881→48.935 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.94
RfactorNum. reflection% reflection
Rfree0.2276 5913 4.96 %
Rwork0.1789 --
obs0.1813 119322 89.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.82 Å2 / Biso mean: 26.5554 Å2 / Biso min: 9.49 Å2
Refinement stepCycle: final / Resolution: 1.881→48.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13268 0 103 971 14342
Biso mean--35.48 27.73 -
Num. residues----1708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713715
X-RAY DIFFRACTIONf_angle_d0.85318647
X-RAY DIFFRACTIONf_chiral_restr0.0542043
X-RAY DIFFRACTIONf_plane_restr0.0062468
X-RAY DIFFRACTIONf_dihedral_angle_d4.67111043
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8814-1.90280.35391140.3509192646
1.9028-1.92520.38021100.3216211651
1.9252-1.94860.38561220.2951238958
1.9486-1.97330.33561580.2715260163
1.9733-1.99930.30871440.2715283968
1.9993-2.02670.33551470.2717296771
2.0267-2.05560.30451700.2567319777
2.0556-2.08630.30951900.2411342682
2.0863-2.11890.31511680.2334372789
2.1189-2.15360.30551900.2287393594
2.1536-2.19080.27562230.2266410899
2.1908-2.23060.27922290.22024165100
2.2306-2.27350.2962160.21154187100
2.2735-2.31990.28182250.2024122100
2.3199-2.37040.24012160.20084178100
2.3704-2.42550.25172240.2014186100
2.4255-2.48620.23832050.19814194100
2.4862-2.55340.25822140.1964184100
2.5534-2.62850.26152220.1854179100
2.6285-2.71340.23552140.18824198100
2.7134-2.81030.25771950.18384230100
2.8103-2.92280.2482140.18134207100
2.9228-3.05580.20122380.17934175100
3.0558-3.21690.2282020.1844420899
3.2169-3.41840.21462100.174253100
3.4184-3.68230.19852130.15414236100
3.6823-4.05270.182230.14034241100
4.0527-4.63870.18652480.12854257100
4.6387-5.84280.16212500.12994305100
5.8428-48.930.17622190.1428447399

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