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- PDB-7rb1: Isocitrate Lyase-1 from Mycobacterium tuberculosis covalently mod... -

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Basic information

Entry
Database: PDB / ID: 7rb1
TitleIsocitrate Lyase-1 from Mycobacterium tuberculosis covalently modified by 5-descarboxy-5-nitro-D-isocitric acid
ComponentsIsocitrate lyase
KeywordsLYASE / tuberculosis / glyoxylate shunt / inhibitor
Function / homology
Function and homology information


methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region ...methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / 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
dihydroxyacetic acid / (3E)-3-(hydroxyimino)propanoic acid / GLYOXYLIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKrieger, I.V. / Mellott, D. / Meek, T. / Sacchettini, J.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Mechanism-Based Inactivation of Mycobacterium tuberculosis Isocitrate Lyase 1 by (2 R ,3 S )-2-Hydroxy-3-(nitromethyl)succinic acid.
Authors: Mellott, D.M. / Torres, D. / Krieger, I.V. / Cameron, S.A. / Moghadamchargari, Z. / Laganowsky, A. / Sacchettini, J.C. / Meek, T.D. / Harris, L.D.
History
DepositionJul 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)190,23128
Polymers188,5384
Non-polymers1,69424
Water14,592810
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35300 Å2
ΔGint-222 kcal/mol
Surface area49680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.068, 140.301, 160.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 47134.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: icl, Rv0467, MTV038.11 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WKK7, isocitrate lyase

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Non-polymers , 6 types, 834 molecules

#2: Chemical ChemComp-48J / dihydroxyacetic acid / glyoxylate hydrate


Mass: 92.051 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-54I / (3E)-3-(hydroxyimino)propanoic acid


Mass: 103.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.0), 0.2 M sodium acetate, and 20-30% PEG4000

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Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→80 Å / Num. obs: 133991 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.21 Å2 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.076 / Rrim(I) all: 0.194 / Χ2: 1.102 / Net I/σ(I): 4 / Num. measured all: 861565
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.935.91.666200.4210.7141.7550.51399.6
1.93-1.9761.38765980.5280.6091.5170.53399.6
1.97-2.016.11.16766040.6150.5091.2750.56199.6
2.01-2.056.21.04366130.6470.4511.1380.58299.5
2.05-2.096.30.86366740.7370.3710.9410.66999.5
2.09-2.146.40.77366030.7810.3270.840.69499.4
2.14-2.196.10.66465900.7950.2910.7260.75899.1
2.19-2.256.50.58366230.8480.2440.6330.84499.7
2.25-2.326.70.51366530.8720.210.5550.88799.8
2.32-2.396.70.44966850.9070.1850.4860.94100
2.39-2.486.70.37566750.910.1560.4070.99799.9
2.48-2.586.60.31666890.9310.1330.3441.10799.9
2.58-2.76.10.26166990.950.1140.2851.1499.6
2.7-2.846.90.22366710.9740.0910.2411.186100
2.84-3.026.90.17767480.9810.0730.1921.341100
3.02-3.256.80.14867240.9870.0610.161.4299.9
3.25-3.586.30.11867630.9890.0510.1291.71699.8
3.58-4.096.90.09967930.9920.0410.1071.94399.9
4.09-5.166.40.08768490.9930.0370.0941.89499.9
5.16-806.30.09771170.9870.0430.1071.93599.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VB9

6vb9


Resolution: 1.9→42.57 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6032
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 6645 4.96 %
Rwork0.1705 127201 -
obs0.1722 133846 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13232 0 107 810 14149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009113658
X-RAY DIFFRACTIONf_angle_d1.037518553
X-RAY DIFFRACTIONf_chiral_restr0.06152027
X-RAY DIFFRACTIONf_plane_restr0.00662454
X-RAY DIFFRACTIONf_dihedral_angle_d21.89474905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.30812250.25524097X-RAY DIFFRACTION96.71
1.92-1.940.29542200.25764142X-RAY DIFFRACTION99.54
1.94-1.970.30272290.24054214X-RAY DIFFRACTION99.64
1.97-1.990.27292300.23514193X-RAY DIFFRACTION99.59
1.99-2.020.26722040.23084174X-RAY DIFFRACTION99.32
2.02-2.040.27152150.2244184X-RAY DIFFRACTION99.68
2.04-2.070.26722370.22964214X-RAY DIFFRACTION99.35
2.07-2.110.27392110.21774172X-RAY DIFFRACTION99.61
2.11-2.140.26172090.20694243X-RAY DIFFRACTION99.42
2.14-2.170.24092190.19764157X-RAY DIFFRACTION99.12
2.17-2.210.26552310.20054202X-RAY DIFFRACTION99.24
2.21-2.250.21432070.19714186X-RAY DIFFRACTION99.8
2.25-2.290.26062250.20214238X-RAY DIFFRACTION99.75
2.29-2.340.25542200.19554242X-RAY DIFFRACTION99.87
2.34-2.390.26052340.1944186X-RAY DIFFRACTION99.95
2.39-2.450.23272150.19084242X-RAY DIFFRACTION99.93
2.45-2.510.22742400.18464264X-RAY DIFFRACTION99.91
2.51-2.580.23922210.18464195X-RAY DIFFRACTION99.84
2.58-2.650.22462090.18134251X-RAY DIFFRACTION99.64
2.65-2.740.21392110.17684230X-RAY DIFFRACTION99.71
2.74-2.840.22482450.17714226X-RAY DIFFRACTION100
2.84-2.950.20952120.17074275X-RAY DIFFRACTION100
2.95-3.080.19282070.17384263X-RAY DIFFRACTION99.93
3.08-3.250.19822220.17974283X-RAY DIFFRACTION99.93
3.25-3.450.19392110.16194289X-RAY DIFFRACTION99.78
3.45-3.720.18012070.15124318X-RAY DIFFRACTION99.91
3.72-4.090.16572190.13484316X-RAY DIFFRACTION99.93
4.09-4.680.17362300.13014350X-RAY DIFFRACTION99.98
4.68-5.890.16272280.13764366X-RAY DIFFRACTION99.85
5.89-42.570.14182520.15014489X-RAY DIFFRACTION98.71

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