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- PDB-6t5m: Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 6t5m
TitleCrystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in complex with Mg(II)-pyruvate.
Components2-methylisocitrate lyase
KeywordsLYASE / 2-methlyisocitrate lyase / PrpB / Propionate metabolism
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
PYRUVIC ACID / 2-methylisocitrate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M019411/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/R005435/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of 2-methylisocitrate lyase (PrpB) from Pseudomonas aeruginosa in complex with Mg(II)-pyruvate.
Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)129,14412
Polymers128,6954
Non-polymers4498
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20760 Å2
ΔGint-99 kcal/mol
Surface area37410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.490, 59.400, 147.650
Angle α, β, γ (deg.)90.000, 120.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-503-

HOH

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Components

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


Mass: 32173.752 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: prpB, PA0796 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I5E2, methylisocitrate lyase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: PrpB 13-15 mg/ml with 5 mM DTT 0.1 M TRIS 8.5 pH (Buffer) 20-30 %w/v PEG4K (Precipitant) 0.1-0.25 M LiSO4 (Salt)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.76→63.74 Å / Num. obs: 97480 / % possible obs: 85.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 27.84 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.069 / Rrim(I) all: 0.118 / Net I/σ(I): 8.5 / Num. measured all: 234810 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.812.10.7881.174370.4540.6111.00388.6
7.87-63.742.30.06610030.9650.050.08373.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T4V

6t4v


Resolution: 1.76→42.493 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.09
RfactorNum. reflection% reflection
Rfree0.2268 4805 4.93 %
Rwork0.211 --
obs0.2118 97414 85.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.06 Å2 / Biso mean: 32.4167 Å2 / Biso min: 13.07 Å2
Refinement stepCycle: final / Resolution: 1.76→42.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8346 0 28 490 8864
Biso mean--32.57 30.82 -
Num. residues----1105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158559
X-RAY DIFFRACTIONf_angle_d1.81111611
X-RAY DIFFRACTIONf_chiral_restr0.0931377
X-RAY DIFFRACTIONf_plane_restr0.011528
X-RAY DIFFRACTIONf_dihedral_angle_d16.3823095
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.76-1.780.40161700.3904313187
1.78-1.8010.37671640.3627319189
1.801-1.82290.3541510.3332320289
1.8229-1.8460.32261820.3364319589
1.846-1.87030.33511590.3273322689
1.8703-1.89590.50991490.4369317088
1.8959-1.9230.47411810.4176315688
1.923-1.95170.35471570.3333310988
1.9517-1.98220.28971990.2631313488
1.9822-2.01470.26661730.2339313687
2.0147-2.04940.26171620.2269312887
2.0494-2.08670.26461460.2359307385
2.0867-2.12680.24371620.2284316787
2.1268-2.17020.24511490.2238309987
2.1702-2.21740.27711370.253315686
2.2174-2.2690.34351620.3261302784
2.269-2.32570.28011830.2354304586
2.3257-2.38860.22421520.1956314086
2.3886-2.45890.24041430.1962308685
2.4589-2.53830.21661700.1902300684
2.5383-2.6290.20051480.1931311785
2.629-2.73420.22881800.1998308485
2.7342-2.85860.22581630.198302185
2.8586-3.00930.22331410.2036305884
3.0093-3.19780.22881470.2099302783
3.1978-3.44460.22661630.196298982
3.4446-3.7910.17951570.1873295682
3.791-4.33910.15241480.1595294080
4.3391-5.4650.16191590.1431293980
5.465-42.4930.15921480.175290177

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