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- PDB-9hhs: Crystal Structure of the Coxiella burnetii R152Q Mutant 2-methyli... -

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Basic information

Entry
Database: PDB / ID: 9hhs
TitleCrystal Structure of the Coxiella burnetii R152Q Mutant 2-methylisocitrate lyase
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
CITRIC ACID / 2-methylisocitrate lyase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 22, 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)69,1969
Polymers68,6582
Non-polymers5387
Water4,630257
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)138,39218
Polymers137,3164
Non-polymers1,07614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area25320 Å2
ΔGint-102 kcal/mol
Surface area43180 Å2
Unit cell
Length a, b, c (Å)73.940, 73.940, 184.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 34329.102 Da / Num. of mol.: 2 / Mutation: R152Q
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
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 10% v/v EtOH, 0.1 M sodium-citrate pH 4.2, 1% w/w PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.7→52.58 Å / Num. obs: 65204 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.9995 / Net I/σ(I): 17.62
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 3221 / CC1/2: 0.3025

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→52.58 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.498 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 3243 5 %RANDOM
Rwork0.21042 ---
obs0.21294 61891 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å2-0 Å2
3----1.49 Å2
Refinement stepCycle: 1 / Resolution: 1.7→52.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 34 257 4790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6366329
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.165603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6523.021235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32315788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5851526
X-RAY DIFFRACTIONr_chiral_restr0.110.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023525
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_it9.03310.5052370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.73719.5512966
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it11.31611.6212289
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined16.23777.0766945
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: 8769 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 228 -
Rwork0.41 4503 -
obs--99.98 %

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