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- PDB-7cp1: Crystal structure of isocitrate lyase in complex with succinate a... -

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Basic information

Entry
Database: PDB / ID: 7cp1
TitleCrystal structure of isocitrate lyase in complex with succinate and itaconate
ComponentsIsocitrate lyase
KeywordsLYASE / Glyoxylate cycle / Isocitrate lyase / Succinate / Itaconate / Mycobacterium tuberculosis
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. / 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
2-methylidenebutanedioic acid / SUCCINIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsKwon, S. / Park, H.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017M3A9D8062960
National Research Foundation (NRF, Korea)2018R1A4A1023822 Korea, Republic Of
CitationJournal: Plos One / Year: 2021
Title: Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism.
Authors: Kwon, S. / Chun, H.L. / Ha, H.J. / Lee, S.Y. / Park, H.H.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,7086
Polymers96,4112
Non-polymers2974
Water11,367631
1
A: Isocitrate lyase
B: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
B: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,41612
Polymers192,8224
Non-polymers5948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area30000 Å2
ΔGint-185 kcal/mol
Surface area52550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.320, 131.320, 284.882
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

21B-676-

HOH

31B-726-

HOH

41B-823-

HOH

51B-903-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 418)
21(chain B and (resid 2 through 192 or (resid 193...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU(chain A and resid 2 through 418)AA2 - 4182 - 418
21SERSERGLYGLY(chain B and (resid 2 through 192 or (resid 193...BB2 - 1922 - 192
22HISHISLEULEU(chain B and (resid 2 through 192 or (resid 193...BB193 - 194193 - 194
23SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
24SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
25SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
26SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
Detailsdimer in the aymmetric unit; tetramer in solution

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Components

#1: Protein Isocitrate lyase / ICL / Isocitrase / Isocitratase


Mass: 48205.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Some parts at the ends were not assigned due to poor electron density.
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: icl, Rv0467, MTV038.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WKK7, isocitrate lyase
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ITN / 2-methylidenebutanedioic acid


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 3.68 Å3/Da / Density % sol: 66.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.6 M sodium phosphate, 1.2 M potassium phosphate, 0.1 M imidazole (pH 8.5), 250 mM sodium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9779 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.577→50 Å / Num. obs: 44429 / % possible obs: 95.1 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.043 / Rrim(I) all: 0.158 / Χ2: 0.93 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.58-2.649.40.6728000.8220.1930.7020.92592.4
2.64-2.719.80.5828590.8630.1610.6060.96394
2.71-2.789.70.50329000.8760.1410.5260.97694.9
2.78-2.8610.10.43629360.9060.1190.4561.01496
2.86-2.9510.20.38229340.9230.1040.41.03396.4
2.95-3.069.40.32129850.950.0890.3371.05197
3.06-3.188.70.27529760.960.0810.291.11397.2
3.18-3.3380.20329720.9750.0630.2151.01597.1
3.33-3.57.20.16829840.9820.0570.1790.96396.6
3.5-3.726.70.13329950.9870.050.1430.90896.3
3.72-4.016.80.11430010.990.0450.1230.80796.2
4.01-4.417.70.10829690.9910.0390.1160.81594.7
4.41-5.059.70.09629350.9940.030.1010.86692.9
5.05-6.3615.80.10329600.9960.0250.1060.85192.4
6.36-5025.90.06632230.9990.0130.0680.84893.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8M

1f8m


Resolution: 2.58→43.033 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 2119 4.92 %
Rwork0.1536 40952 -
obs0.1556 43071 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.14 Å2 / Biso mean: 32.997 Å2 / Biso min: 15.55 Å2
Refinement stepCycle: final / Resolution: 2.58→43.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 19 641 7102
Biso mean--37.94 36.36 -
Num. residues----832
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2538X-RAY DIFFRACTION3.879TORSIONAL
12B2538X-RAY DIFFRACTION3.879TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.58-2.63740.27931340.228263991
2.6374-2.70330.23211300.206271894
2.7033-2.77640.23111530.2017274995
2.7764-2.85810.28171540.1926277396
2.8581-2.95030.26691430.1863278896
2.9503-3.05570.22561420.1804283597
3.0557-3.1780.27531330.1868285497
3.178-3.32260.19611500.1569281797
3.3226-3.49770.1991420.1513283996
3.4977-3.71670.19951540.142282796
3.7167-4.00350.18311480.1287285096
4.0035-4.40610.16561350.1278281394
4.4061-5.04280.14561510.1214275892
5.0428-6.35010.161070.1356249081
6.3501-43.0330.13211430.1321220269

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