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- PDB-1ujq: Crystal structure of 2-methylisocitrate lyase (PrpB) from Salmone... -

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Basic information

Entry
Database: PDB / ID: 1ujq
TitleCrystal structure of 2-methylisocitrate lyase (PrpB) from Salmonella enterica serovar typhimurium
ComponentsProbable methylisocitrate lyase
KeywordsLYASE / PRPB / METHYLISOCITRATE / METHYLCITRATE CYCLE / TIM-2 BARREL
Function / homology
Function and homology information


methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / molecular function activator activity / magnesium ion binding
Similarity search - Function
2-methylisocitrate lyase / Phosphoenolpyruvate phosphomutase / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-methylisocitrate lyase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSimanshu, D.K. / Murthy, M.R.N.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Crystal structure of Salmonella typhimurium 2-methylisocitrate lyase (PrpB) and its complex with pyruvate and Mg(2+)
Authors: Simanshu, D.K. / Satheshkumar, P.S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionAug 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Probable methylisocitrate lyase
B: Probable methylisocitrate lyase
C: Probable methylisocitrate lyase
D: Probable methylisocitrate lyase


Theoretical massNumber of molelcules
Total (without water)133,0594
Polymers133,0594
Non-polymers00
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17040 Å2
ΔGint-80 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.812, 99.086, 201.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable methylisocitrate lyase / 2-methylisocitrate lyase


Mass: 33264.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Species: Salmonella enterica / Strain: IFO 12529 / Gene: prpB / Plasmid: pET-Blue vector(Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q56062, methylisocitrate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5551.39
2
3
4
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop6.5Imidazole,Sodium acetate trihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop8Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2913vapor diffusion, sitting drop8Sodium chloride, PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
2774vapor diffusion, sitting drop4.5Sodium formate, Sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Mimidazole1reservoirpH6.5
21.0 Msodium acetate trihydrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2003 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 74393 / Num. obs: 69022 / % possible obs: 92.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 5.2 / Num. unique all: 7079 / Rsym value: 0.423 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 70807 / % possible obs: 95.4 % / Num. measured all: 391895
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.423

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUM

1mum


Resolution: 2.1→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 499934.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Coordinates of the residues ranging from 87 to 96 in the D subunit are tentative due to poor electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3514 5.1 %RANDOM
Rwork0.205 ---
obs0.205 69022 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.8205 Å2 / ksol: 0.364637 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å20 Å2
2--6.09 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8220 0 0 565 8785
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 575 5.2 %
Rwork0.243 10493 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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