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- PDB-5e9f: Structural insights of isocitrate lyases from Magnaporthe oryzae -

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Basic information

Entry
Database: PDB / ID: 5e9f
TitleStructural insights of isocitrate lyases from Magnaporthe oryzae
ComponentsIsocitrate lyase
KeywordsLYASE / TIM BETA/ALPHA-BARREL / LYASE ACTIVITY
Function / homology
Function and homology information


glyoxysome / methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #850 / 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 / Arc Repressor Mutant, subunit A / TIM Barrel ...Arc Repressor Mutant, subunit A - #850 / 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 / Arc Repressor Mutant, subunit A / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMagnaporthe oryzae 70-15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPark, Y. / Cho, Y. / Lee, Y.-H. / Lee, Y.-W. / Rhee, S.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum
Authors: Park, Y. / Cho, Y. / Lee, Y.-H. / Lee, Y.-W. / Rhee, S.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)250,6568
Polymers250,5594
Non-polymers974
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31830 Å2
ΔGint-212 kcal/mol
Surface area66970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.583, 135.314, 158.880
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 / ISOCITRASE / Isocitratase / Methylisocitrate lyase / MICA / Threo-D(S)-isocitrate glyoxylate-lyase


Mass: 62639.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae 70-15 (fungus) / Strain: 70-15 / Gene: ICL1, MGG_04895 / Production host: Escherichia coli (E. coli)
References: UniProt: P0CT06, isocitrate lyase, methylisocitrate lyase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M SODIUM MALONATE, 20% PEG 3350, 10% (V/V) GLYCEROL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.964 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 64146 / % possible obs: 99.47 % / Redundancy: 7.4 % / Net I/σ(I): 11.18
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQU

1dqu


Resolution: 2.8→32.4 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1998 3.12 %
Rwork0.186 --
obs0.187 64136 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14914 0 4 66 14984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915266
X-RAY DIFFRACTIONf_angle_d1.14320790
X-RAY DIFFRACTIONf_dihedral_angle_d14.1555408
X-RAY DIFFRACTIONf_chiral_restr0.0452303
X-RAY DIFFRACTIONf_plane_restr0.0062704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.809-2.87970.34391330.24464117X-RAY DIFFRACTION93
2.8797-2.95750.32191400.23034381X-RAY DIFFRACTION100
2.9575-3.04450.3041420.21874395X-RAY DIFFRACTION100
3.0445-3.14270.33781420.22034418X-RAY DIFFRACTION100
3.1427-3.2550.28531420.21474406X-RAY DIFFRACTION100
3.255-3.38520.2781430.21384454X-RAY DIFFRACTION100
3.3852-3.53920.27331420.19424405X-RAY DIFFRACTION100
3.5392-3.72560.23921430.1814445X-RAY DIFFRACTION100
3.7256-3.95870.25481440.1834455X-RAY DIFFRACTION100
3.9587-4.2640.2271420.16834459X-RAY DIFFRACTION100
4.264-4.69220.20021440.1654472X-RAY DIFFRACTION100
4.6922-5.36930.20841450.17684498X-RAY DIFFRACTION100
5.3693-6.75760.31241470.24314547X-RAY DIFFRACTION100
6.7576-36.22610.27761510.24634694X-RAY DIFFRACTION100

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