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- PDB-1f8i: CRYSTAL STRUCTURE OF ISOCITRATE LYASE:NITROPROPIONATE:GLYOXYLATE ... -

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Basic information

Entry
Database: PDB / ID: 1f8i
TitleCRYSTAL STRUCTURE OF ISOCITRATE LYASE:NITROPROPIONATE:GLYOXYLATE COMPLEX FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsISOCITRATE LYASE
KeywordsLYASE / AlPHA-BETA Barrel / Swapped Helices / closed conformation / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


methylisocitrate lyase / methylisocitrate lyase activity / glyoxysome / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle ...methylisocitrate lyase / methylisocitrate lyase activity / glyoxysome / 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. / 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 / SUCCINIC ACID / Isocitrate lyase 1 / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsSharma, V. / Sharma, S. / Hoener zu Bentrup, K. / McKinney, J.D. / Russell, D.G. / Jacobs Jr., W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.
Authors: Sharma, V. / Sharma, S. / Hoener zu Bentrup, K. / McKinney, J.D. / Russell, D.G. / Jacobs Jr., W.R. / Sacchettini, J.C.
History
DepositionJun 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)189,62316
Polymers188,7584
Non-polymers86612
Water18,9521052
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34790 Å2
ΔGint-160 kcal/mol
Surface area48790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.291, 129.018, 166.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ISOCITRATE LYASE / ICL


Mass: 47189.410 Da / Num. of mol.: 4 / Mutation: C191S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: PET30B / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5H3, UniProt: P9WKK7*PLUS, isocitrate lyase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1052 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 289 K / Method: microbatch under paraffin oil / pH: 8
Details: PEG4000, sodium acetate, Tris.HCl, magnesium acetate, glyoxylate, 3-nitropropionate, pH 8.0, Microbatch under Paraffin oil, temperature 289.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
20.2 Msodium acetate1reservoir
320-30 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→99 Å / Num. all: 75213 / Num. obs: 72007 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.12 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 0.122 / Num. unique all: 6128 / % possible all: 79.8
Reflection
*PLUS
Num. measured all: 296878 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 79.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 2.25→35.02 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 199873.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 7263 10.1 %RANDOM
Rwork0.166 ---
all0.175 71997 --
obs0.166 71739 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.37 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20 Å2
2--2.02 Å20 Å2
3----5.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.25→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13232 0 56 1052 14340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.62.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 1078 10 %
Rwork0.192 9753 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3LIG.PARLIG.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.249 / % reflection Rfree: 10 % / Rfactor Rwork: 0.192

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