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- PDB-5dql: Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase... -

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Basic information

Entry
Database: PDB / ID: 5dql
TitleCrystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis
ComponentsIsocitrate lyase 1
KeywordsLYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


methylisocitrate lyase / glyoxysome / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle ...methylisocitrate lyase / glyoxysome / 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. / 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
4-hydroxy-2-oxobutanoic acid / Isocitrate lyase 1 / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsHuang, H.-L. / Meek, T.D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis.
Authors: Pham, T.V. / Murkin, A.S. / Moynihan, M.M. / Harris, L. / Tyler, P.C. / Shetty, N. / Sacchettini, J.C. / Huang, H.L. / Meek, T.D.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate lyase 1
B: Isocitrate lyase 1
C: Isocitrate lyase 1
D: Isocitrate lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,13113
Polymers188,5384
Non-polymers5949
Water22,3391240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33720 Å2
ΔGint-165 kcal/mol
Surface area49600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.086, 129.236, 167.952
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 1 / ICL1 / Isocitrase / Isocitratase / Methylisocitrate lyase / MICA


Mass: 47134.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) (bacteria)
Strain: ATCC 35801 / TMC 107 / Erdman / Gene: icl1, ERDMAN_0512, Q643_00485 / Plasmid: pET30(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: H8EVV4, UniProt: P9WKK7*PLUS, isocitrate lyase, methylisocitrate lyase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-VGX / 4-hydroxy-2-oxobutanoic acid


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


Mass: 18.015 Da / Num. of mol.: 1240 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 4000, Sodium acetate, Tris-HCl / PH range: 7.5-8.5 / Temp details: Varies between 289-291K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 cryo stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→42.31 Å / Num. obs: 155652 / % possible obs: 99.6 % / Redundancy: 7.7 % / Rsym value: 0.0408 / Net I/σ(I): 14.01
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 0.45 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SBC-CollectSBC CATdata collection
SCALEPACKHKL3000data scaling
CootCOOT 0.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8M

1f8m


Resolution: 1.782→34.274 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 7803 5.03 %Random
Rwork0.2026 ---
obs0.2048 155177 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.782→34.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13232 0 33 1240 14505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813562
X-RAY DIFFRACTIONf_angle_d1.12618434
X-RAY DIFFRACTIONf_dihedral_angle_d15.74854
X-RAY DIFFRACTIONf_chiral_restr0.0762022
X-RAY DIFFRACTIONf_plane_restr0.0052440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.782-1.80220.40642110.38034221X-RAY DIFFRACTION86
1.8022-1.82340.39072610.37214785X-RAY DIFFRACTION98
1.8234-1.84570.40822420.36314881X-RAY DIFFRACTION99
1.8457-1.8690.38132430.33674893X-RAY DIFFRACTION100
1.869-1.89360.41462630.3244863X-RAY DIFFRACTION100
1.8936-1.91960.34622720.30694888X-RAY DIFFRACTION100
1.9196-1.9470.32812390.29824908X-RAY DIFFRACTION100
1.947-1.97610.34192580.2894932X-RAY DIFFRACTION100
1.9761-2.00690.35622610.28154871X-RAY DIFFRACTION100
2.0069-2.03980.34922550.28194917X-RAY DIFFRACTION100
2.0398-2.0750.31882400.27334934X-RAY DIFFRACTION100
2.075-2.11270.33322520.26254911X-RAY DIFFRACTION100
2.1127-2.15340.30752690.26014924X-RAY DIFFRACTION100
2.1534-2.19730.30982670.2554880X-RAY DIFFRACTION100
2.1973-2.24510.3482540.25834897X-RAY DIFFRACTION100
2.2451-2.29730.29452560.24924965X-RAY DIFFRACTION100
2.2973-2.35470.31062580.24544918X-RAY DIFFRACTION100
2.3547-2.41840.34392710.23014938X-RAY DIFFRACTION100
2.4184-2.48950.28922710.22434882X-RAY DIFFRACTION100
2.4895-2.56980.27542670.21734917X-RAY DIFFRACTION100
2.5698-2.66170.28932820.21624929X-RAY DIFFRACTION100
2.6617-2.76820.2622490.21364974X-RAY DIFFRACTION100
2.7682-2.89410.28362620.21014963X-RAY DIFFRACTION100
2.8941-3.04660.25512540.2064955X-RAY DIFFRACTION100
3.0466-3.23730.25362650.20974975X-RAY DIFFRACTION100
3.2373-3.48710.24742750.20094957X-RAY DIFFRACTION100
3.4871-3.83760.19952700.17345014X-RAY DIFFRACTION100
3.8376-4.39190.18372850.15585018X-RAY DIFFRACTION100
4.3919-5.52960.1962730.14855059X-RAY DIFFRACTION100
5.5296-34.28010.1672780.15145205X-RAY DIFFRACTION99

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