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- PDB-8z1r: isocitrate lyase MoMcl1 -

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Basic information

Entry
Database: PDB / ID: 8z1r
Titleisocitrate lyase MoMcl1
ComponentsIsocitrate lyase
KeywordsLYASE / e.g.Complex
Function / homology
Function and homology information


propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / isocitrate lyase activity / mitochondrial matrix / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesPyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLiu, X.H. / Zhao, W.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2023YFD1400202-3 China
CitationJournal: To Be Published
Title: High-resolution crystal structure of the MoMcl1 protein
Authors: Liu, X.H. / Zhao, W.H.
History
DepositionApr 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4497
Polymers123,2142
Non-polymers2355
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-61 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.430, 150.495, 128.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1036-

HOH

21A-1047-

HOH

31B-857-

HOH

41B-1058-

HOH

51B-1111-

HOH

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Components

#1: Protein Isocitrate lyase


Mass: 61606.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Strain: Pyricularia oryzae / Gene: MGCH7_ch7g337 / Variant: 318829 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EH03
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 4% v/v TacsimateTM pH 8.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.82→32.81 Å / Num. obs: 102343 / % possible obs: 99.96 % / Redundancy: 12.2 % / Biso Wilson estimate: 33.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1357 / Rpim(I) all: 0.04074 / Rrim(I) all: 0.1418 / Net I/σ(I): 14.46
Reflection shellResolution: 1.82→1.885 Å / Num. unique obs: 10172 / CC1/2: 0.727 / Rpim(I) all: 0.5381

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→32.81 Å / SU ML: 0.2032 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 5021 4.91 %
Rwork0.184 97303 -
obs0.1856 102324 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.1 Å2
Refinement stepCycle: LAST / Resolution: 1.82→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8001 0 14 735 8750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00638214
X-RAY DIFFRACTIONf_angle_d0.76511148
X-RAY DIFFRACTIONf_chiral_restr0.05121201
X-RAY DIFFRACTIONf_plane_restr0.00811458
X-RAY DIFFRACTIONf_dihedral_angle_d13.61162973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.32451590.28553252X-RAY DIFFRACTION99.97
1.84-1.860.31121920.27083152X-RAY DIFFRACTION99.97
1.86-1.890.3051830.26573231X-RAY DIFFRACTION99.97
1.89-1.910.30651550.24623209X-RAY DIFFRACTION99.97
1.91-1.930.2851450.2443204X-RAY DIFFRACTION100
1.93-1.960.27971620.2393246X-RAY DIFFRACTION99.94
1.96-1.990.24431530.22233228X-RAY DIFFRACTION100
1.99-2.020.24941820.21813171X-RAY DIFFRACTION99.94
2.02-2.050.23351430.21413268X-RAY DIFFRACTION100
2.05-2.080.23211780.21363225X-RAY DIFFRACTION100
2.08-2.120.24251650.19693187X-RAY DIFFRACTION99.94
2.12-2.160.21081700.18763219X-RAY DIFFRACTION99.97
2.16-2.20.20651510.1853228X-RAY DIFFRACTION100
2.2-2.240.20071480.18733268X-RAY DIFFRACTION100
2.24-2.290.2311740.1843216X-RAY DIFFRACTION100
2.29-2.350.19721760.18823215X-RAY DIFFRACTION100
2.35-2.40.22691800.19263228X-RAY DIFFRACTION100
2.4-2.470.23081610.19033257X-RAY DIFFRACTION100
2.47-2.540.2141590.19023215X-RAY DIFFRACTION100
2.54-2.620.1881550.18463258X-RAY DIFFRACTION100
2.62-2.720.21791870.1983231X-RAY DIFFRACTION100
2.72-2.830.23911720.19743236X-RAY DIFFRACTION100
2.83-2.960.24721690.19283254X-RAY DIFFRACTION100
2.96-3.110.22611640.19193253X-RAY DIFFRACTION99.97
3.11-3.310.19011710.18943271X-RAY DIFFRACTION100
3.31-3.560.2091760.17563261X-RAY DIFFRACTION100
3.56-3.920.18911870.15343235X-RAY DIFFRACTION100
3.92-4.480.16261610.15193319X-RAY DIFFRACTION100
4.49-5.650.2191570.15573346X-RAY DIFFRACTION100
5.65-32.810.20221860.16463420X-RAY DIFFRACTION99.72

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