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- PDB-1dqu: CRYSTAL STRUCTURE OF THE ISOCITRATE LYASE FROM ASPERGILLUS NIDULANS -

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Basic information

Entry
Database: PDB / ID: 1dqu
TitleCRYSTAL STRUCTURE OF THE ISOCITRATE LYASE FROM ASPERGILLUS NIDULANS
ComponentsISOCITRATE LYASE
KeywordsLYASE / BETA BARREL
Function / homology
Function and homology information


glyoxysome / acetate catabolic process / methylisocitrate lyase / isocitrate lyase / methylisocitrate lyase activity / isocitrate lyase activity / carbon utilization / fatty acid catabolic process / glyoxylate cycle / peroxisomal matrix ...glyoxysome / acetate catabolic process / methylisocitrate lyase / isocitrate lyase / methylisocitrate lyase activity / isocitrate lyase activity / carbon utilization / fatty acid catabolic process / glyoxylate cycle / peroxisomal matrix / tricarboxylic acid cycle / peroxisome / 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 speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsBritton, K.L. / Langridge, S.J. / Baker, P.J. / Weeradechapon, K. / Sedelnikova, S.E. / De Lucas, J.R. / Rice, D.W. / Turner, G.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
Authors: Britton, K. / Langridge, S. / Baker, P.J. / Weeradechapon, K. / Sedelnikova, S.E. / De Lucas, J.R. / Rice, D.W. / Turner, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Isocitrate Lyase from Aspergillus Nidulans: Crystallization and X-ray Analysis of a Glyoxylate Cycle Enzyme.
Authors: Langridge, S.J. / Baker, P.J. / De Lucas, J.R. / Sedelnikova, S.E. / Turner, G. / Rice, D.W.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOCITRATE LYASE


Theoretical massNumber of molelcules
Total (without water)60,3981
Polymers60,3981
Non-polymers00
Water00
1
A: ISOCITRATE LYASE

A: ISOCITRATE LYASE

A: ISOCITRATE LYASE

A: ISOCITRATE LYASE


Theoretical massNumber of molelcules
Total (without water)241,5934
Polymers241,5934
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area30360 Å2
ΔGint-190 kcal/mol
Surface area75440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.930, 91.930, 152.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe biological assembly is a tetramer constructed from chain A generated by 222 symmetry

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Components

#1: Protein ISOCITRATE LYASE


Mass: 60398.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Description: MULTICOPY INSERTION OF VECTOR INTO CHROMOSOME / Production host: Emericella nidulans (mold) / References: UniProt: P28298, isocitrate lyase

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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: 53.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Langridge, S.J., (1997) Acta Crystallogr., Sect.D, 53, 488.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
21-20 %(w/v)PEG20001drop
30.1 Msodium HEPES1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 27, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 21252 / Num. obs: 21252 / % possible obs: 91.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.439 / Num. unique all: 1198 / % possible all: 71.9
Reflection
*PLUS
Num. measured all: 62390

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Processing

Software
NameVersionClassification
MLPHAREphasing
TNTrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.8→10 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.376 818 -RANDOM
Rwork0.273 ---
all0.276 15857 --
obs0.276 15857 97 %-
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 0 0 4069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.5
X-RAY DIFFRACTIONt_bond_d0.013
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor all: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.5
X-RAY DIFFRACTIONt_planar_d0.011
X-RAY DIFFRACTIONt_plane_restr0.009

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