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- PDB-1igw: Crystal Structure of the Isocitrate Lyase from the A219C mutant o... -

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Basic information

Entry
Database: PDB / ID: 1igw
TitleCrystal Structure of the Isocitrate Lyase from the A219C mutant of Escherichia coli
ComponentsIsocitrate lyase
KeywordsLYASE / BETA BARREL
Function / homology
Function and homology information


isocitrate lyase / cation binding / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / cytosol
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / 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
: / PYRUVIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBritton, K.L. / Abeysinghe, I.S.B. / Baker, P.J. / Barynin, V. / Diehl, P. / Langridge, S.J. / McFadden, B.A. / Sedelnikova, S.E. / Stillman, T.J. / Weeradechapon, K. / Rice, D.W.
Citation
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Use of Chemical Modification in the Crystallization of Isocitrate Lyase from Escherichia coli
Authors: Abeysinghe, S.I. / Baker, P.J. / Rice, D.W. / Rodgers, H.F. / Stillman, T.J. / Ko, Y.H. / McFadden, B.A. / Nimmo, H.G.
History
DepositionApr 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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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)195,05533
Polymers190,3944
Non-polymers4,66229
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32960 Å2
ΔGint-753 kcal/mol
Surface area52170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.650, 88.650, 199.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe given tetramer defines the biological assembly

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Components

#1: Protein
Isocitrate lyase / ISOCITRASE / ISOCITRATASE / ICL


Mass: 47598.395 Da / Num. of mol.: 4 / Mutation: A219C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceA / Plasmid: pICL / Production host: Escherichia coli (E. coli) / Strain (production host): JE10 / References: UniProt: P0A9G6, isocitrate lyase
#2: Chemical...
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MEPEG 2000, magnesium chloride, ethyl mercury thiosalicylate, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MHEPES1drop
25 mM1dropMgCl2
320-22 %(w/v)mPEG20001reservoir
45 mMEMTS1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1995 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→33.3 Å / Num. all: 188246 / Num. obs: 96329 / % possible obs: 94.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.216 / Num. unique all: 6893 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 188246
Reflection shell
*PLUS
% possible obs: 91.3 % / Num. unique obs: 6893 / Num. measured obs: 13435

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Processing

Software
NameVersionClassification
CCP4model building
TFFCmodel building
DMmodel building
REFMACrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
TFFCphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.235 4666 RANDOM
Rwork0.184 --
all0.187 88762 -
obs0.187 88762 -
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12616 0 61 755 13432
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d1.6
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / Rfactor obs: 0.234

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