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- PDB-5e9g: Structural insights of isocitrate lyases from Magnaporthe oryzae -

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Basic information

Entry
Database: PDB / ID: 5e9g
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 / isocitrate lyase / methylisocitrate lyase activity / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
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 / Isocitrate lyase
Similarity search - Component
Biological speciesMagnaporthe oryzae 70-15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _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

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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)251,17315
Polymers250,5034
Non-polymers67011
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35290 Å2
ΔGint-206 kcal/mol
Surface area68880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.122, 135.078, 158.704
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: 62625.793 Da / Num. of mol.: 4 / Mutation: A219G
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-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H2O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M POTASSIUM SODIUM TARTRATE, 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: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 142312 / % possible obs: 93.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.404 / % possible all: 91.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQU

1dqu


Resolution: 2.1→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.259 13732 9 %
Rwork0.224 --
obs0.224 137814 90.8 %
Solvent computationBsol: 38.49 Å2
Displacement parametersBiso mean: 36.99 Å2
Baniso -1Baniso -2Baniso -3
1--12.562 Å20 Å20 Å2
2---1.407 Å20 Å2
3---13.968 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16063 0 42 304 16409
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1831.5
X-RAY DIFFRACTIONc_mcangle_it1.7572
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.5662.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION5CNS_TOPPAR:CARBOHYDRATE.PARAM
X-RAY DIFFRACTION6GLV.PAR
X-RAY DIFFRACTION7GOL.PAR

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