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- PDB-5e9h: Structural insights of isocitrate lyases from Fusarium graminearum -

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Basic information

Entry
Database: PDB / ID: 5e9h
TitleStructural insights of isocitrate lyases from Fusarium graminearum
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
MALONATE ION / : / Isocitrate lyase
Similarity search - Component
Biological speciesGibberella zeae PH-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate lyase
B: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1014
Polymers123,9442
Non-polymers1572
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-57 kcal/mol
Surface area42780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.475, 124.475, 160.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-872-

HOH

21A-882-

HOH

31B-741-

HOH

41B-742-

HOH

51B-784-

HOH

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Components

#1: Protein Isocitrate lyase / ICL / ISOCITRASE / Isocitratase / Methylisocitrate lyase / MICA / Threo-D(S)-isocitrate glyoxylate-lyase


Mass: 61971.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae PH-1 (fungus) / Strain: PH-1 / Gene: ICL1, FGSG_09896 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4HYR2, isocitrate lyase, methylisocitrate lyase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.4M SODIUM MALONATE, PH 8.0, VAPOR DIFFUSION, SITTING 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: 2.3→50 Å / Num. obs: 64136 / % possible obs: 99.95 % / Redundancy: 21.2 % / Net I/σ(I): 19.87
Reflection shellResolution: 2.3→2.38 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: 2.3→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: 2.3→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8223 0 8 420 8651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088411
X-RAY DIFFRACTIONf_angle_d1.12411394
X-RAY DIFFRACTIONf_dihedral_angle_d15.1363086
X-RAY DIFFRACTIONf_chiral_restr0.0431236
X-RAY DIFFRACTIONf_plane_restr0.0061480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35760.2861440.21644382X-RAY DIFFRACTION100
2.3576-2.42140.25611410.21414377X-RAY DIFFRACTION100
2.4214-2.49260.31431400.22624391X-RAY DIFFRACTION100
2.4926-2.5730.29091390.21124383X-RAY DIFFRACTION100
2.573-2.66490.27641440.21254403X-RAY DIFFRACTION100
2.6649-2.77160.27441390.22194421X-RAY DIFFRACTION100
2.7716-2.89760.28071370.22234408X-RAY DIFFRACTION100
2.8976-3.05030.26861460.21094402X-RAY DIFFRACTION100
3.0503-3.24120.24491400.21334434X-RAY DIFFRACTION100
3.2412-3.49120.22541430.18964440X-RAY DIFFRACTION100
3.4912-3.84210.1911440.17124449X-RAY DIFFRACTION100
3.8421-4.39680.20821480.15474468X-RAY DIFFRACTION100
4.3968-5.53510.18081370.15314521X-RAY DIFFRACTION100
5.5351-32.40640.17221560.16484659X-RAY DIFFRACTION100

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