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- PDB-6edw: Crystal structure of Mycobacterium tuberculosis ICL2 in the apo form -

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Basic information

Entry
Database: PDB / ID: 6edw
TitleCrystal structure of Mycobacterium tuberculosis ICL2 in the apo form
ComponentsIsocitrate lyase 2
KeywordsLYASE
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. / ICL/PEPM domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBashiri, G. / Bhusal, R. / Leung, I.
CitationJournal: Nat Commun / Year: 2019
Title: Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2.
Authors: Bhusal, R.P. / Jiao, W. / Kwai, B.X.C. / Reynisson, J. / Collins, A.J. / Sperry, J. / Bashiri, G. / Leung, I.K.H.
History
DepositionAug 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate lyase 2
B: Isocitrate lyase 2
C: Isocitrate lyase 2
D: Isocitrate lyase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,09516
Polymers350,4644
Non-polymers63112
Water62,4763468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48680 Å2
ΔGint-253 kcal/mol
Surface area106700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.824, 136.078, 138.924
Angle α, β, γ (deg.)90.00, 99.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A12 - 764
2010B12 - 764
1020A12 - 762
2020C12 - 762
1030A12 - 764
2030D12 - 764
1040B12 - 762
2040C12 - 762
1050B12 - 764
2050D12 - 764
1060C12 - 762
2060D12 - 762

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Isocitrate lyase 2 / / ICL2 / Isocitrase / Isocitratase


Mass: 87615.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: icl2, aceA-2, MT1966 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VJU4, isocitrate lyase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3468 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 9% w/v PEG 4K, 18% v/v glycerol, 0.02 M amino acids, 0.1 M MES/imidazole pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→136.98 Å / Num. obs: 323074 / % possible obs: 99.9 % / Redundancy: 7.7 % / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.32 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.22 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20254 16234 5 %RANDOM
Rwork0.16828 ---
obs0.16999 306789 99.85 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.25 Å2
2--0.94 Å20 Å2
3----1.09 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23222 0 37 3468 26727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01423892
X-RAY DIFFRACTIONr_bond_other_d0.0010.01721211
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.65932368
X-RAY DIFFRACTIONr_angle_other_deg0.8491.63549747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53852979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61120.8761416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.973153961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.72115239
X-RAY DIFFRACTIONr_chiral_restr0.0520.23049
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0227464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024472
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2582.66611847
X-RAY DIFFRACTIONr_mcbond_other4.2552.66611846
X-RAY DIFFRACTIONr_mcangle_it5.3533.97714796
X-RAY DIFFRACTIONr_mcangle_other5.3533.97714797
X-RAY DIFFRACTIONr_scbond_it6.2823.22312045
X-RAY DIFFRACTIONr_scbond_other6.2813.22312045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4984.59617551
X-RAY DIFFRACTIONr_long_range_B_refined9.833.85728893
X-RAY DIFFRACTIONr_long_range_B_other9.62832.8327649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A242510.06
12B242510.06
21A235560.06
22C235560.06
31A241190.06
32D241190.06
41B236620.07
42C236620.07
51B242440.07
52D242440.07
61C236900.06
62D236900.06
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 1241 -
Rwork0.309 22312 -
obs--98.6 %

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