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- PDB-1oqf: Crystal structure of the 2-methylisocitrate lyase -

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Basic information

Entry
Database: PDB / ID: 1oqf
TitleCrystal structure of the 2-methylisocitrate lyase
Components2-methylisocitrate lyase
KeywordsLYASE / structural genomics / alpha-beta barrel / swapped helix across a dimer / Structure 2 Function Project / S2F
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 / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.93 Å
AuthorsLiu, S. / Lu, Z. / Dunaway-Mariano, D. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution.
Authors: Liu, S. / Lu, Z. / Han, Y. / Melamud, E. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionMar 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)64,0772
Polymers64,0772
Non-polymers00
Water11,674648
1
A: 2-methylisocitrate lyase
B: 2-methylisocitrate lyase

A: 2-methylisocitrate lyase
B: 2-methylisocitrate lyase


Theoretical massNumber of molelcules
Total (without water)128,1544
Polymers128,1544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
Buried area22550 Å2
ΔGint-124 kcal/mol
Surface area39520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.036, 83.036, 166.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 2-methylisocitrate lyase


Mass: 32038.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PRPB OR B0331 / Plasmid: PET3C-PRPB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plys S / References: UniProt: P77541, methylisocitrate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6 M ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 9, 2002 / Details: Harvard Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 52853 / Num. obs: 52853 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 4.35 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.66
Reflection shellResolution: 1.86→1.93 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.11 / Num. unique all: 3824 / % possible all: 68.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
DMmodel building
CNS1refinement
RESOLVEphasing
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.93→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2846 -random
Rwork0.191 ---
all-49029 --
obs-46758 91.9 %-
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4411 0 0 648 5059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5

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