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- PDB-1xg4: Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant fr... -

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Basic information

Entry
Database: PDB / ID: 1xg4
TitleCrystal Structure of the C123S 2-Methylisocitrate Lyase Mutant from Escherichia coli in complex with the inhibitor isocitrate
ComponentsProbable methylisocitrate lyase
KeywordsLYASE / 2-methylisocitrate lyase-inhibitor complex / isocitrate / isocitrate lyase superfamily
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
ISOCITRIC ACID / 2-methylisocitrate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, S. / Lu, Z. / Han, Y. / Melamud, E. / Dunaway-Mariano, D. / Herzberg, O.
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
DepositionSep 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,73910
Polymers128,0894
Non-polymers6496
Water17,691982
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
ΔGint-98 kcal/mol
Surface area36580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.061, 84.561, 99.756
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number5
Space group name H-MC121
Detailsone asymmetric unit has 4 molecules, which form biological assemble of enzyme.

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Components

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


Mass: 32022.355 Da / Num. of mol.: 4 / Mutation: C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prpB / Plasmid: PET3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P77541, methylisocitrate lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG3350, 0.1M (NH)2SO4, 0.1M MES (pH6.0), 5mM Mg(II), 5mM isocitrate acid, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.92139 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92139 Å / Relative weight: 1
ReflectionResolution: 1.55→47.29 Å / Num. obs: 161348 / % possible obs: 88.8 % / Observed criterion σ(I): 1 / Redundancy: 4.16 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.9
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.227 / % possible all: 22.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1oqf

1oqf


Resolution: 1.6→47.29 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4929 -random
Rwork0.181 ---
all-165330 --
obs-138747 83.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.729 Å20 Å2-0.251 Å2
2---5.958 Å20 Å2
3---3.229 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8694 0 51 973 9718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4itm_xplor_param

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