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- PDB-9hgq: Crystal Structure of the Coxiella burnetii 2-methylisocitrate lya... -

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Basic information

Entry
Database: PDB / ID: 9hgq
TitleCrystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Substrate 2-MIC
Components2-methylisocitrate lyase
KeywordsCYTOSOLIC PROTEIN / PrpB / methylisocitrate lyase / carbon-carbon lyase / EC 4.1.3.30
Function / homology
Function and homology information


methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / magnesium ion binding
Similarity search - Function
2-methylisocitrate lyase / Phosphoenolpyruvate phosphomutase / 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
ETHANOL / ALPHA-METHYLISOCITRIC ACID / 2-methylisocitrate lyase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStuart, W. / Isupov, M. / Harmer, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structure and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii.
Authors: Stuart, W.S. / Jenkins, C.H. / Ireland, P.M. / Isupov, M.N. / Norville, I.H. / Harmer, N.J.
History
DepositionNov 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-methylisocitrate lyase
B: 2-methylisocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,23229
Polymers68,7162
Non-polymers1,51627
Water4,882271
1
A: 2-methylisocitrate lyase
B: 2-methylisocitrate lyase
hetero molecules

A: 2-methylisocitrate lyase
B: 2-methylisocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,46458
Polymers137,4334
Non-polymers3,03154
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area30810 Å2
ΔGint-208 kcal/mol
Surface area38600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.310, 73.310, 184.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-methylisocitrate lyase / 2-MIC / MICL / (2R / 3S)-2-methylisocitrate lyase


Mass: 34358.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: prpB, CBU_0771 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83DG5, methylisocitrate lyase

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Non-polymers , 6 types, 298 molecules

#2: Chemical ChemComp-MIC / ALPHA-METHYLISOCITRIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: JCSG+ B6: 40% EtOH, 0.1 M Sodium-citrate pH 4.2, 5% PEG 1K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8517 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8517 Å / Relative weight: 1
ReflectionResolution: 1.9→63.49 Å / Num. obs: 46171 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 0.9996 / Net I/σ(I): 14.94
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 2263 / CC1/2: 0.3986

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→63.49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.151 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24295 2219 4.9 %RANDOM
Rwork0.1888 ---
obs0.19157 43130 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.511 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.9→63.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 88 271 4743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124544
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.646124
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35722.756225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21615756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6191526
X-RAY DIFFRACTIONr_chiral_restr0.0940.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023398
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.8379.532290
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.0217.7372860
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.3810.532247
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.08770.2796965
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8495 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 99 -
Rwork0.411 2485 -
obs--77.02 %

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