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- PDB-8sw9: Plasmodium falciparum M17 (A460S) mutant -

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Basic information

Entry
Database: PDB / ID: 8sw9
TitlePlasmodium falciparum M17 (A460S) mutant
ComponentsLeucine aminopeptidase
KeywordsHYDROLASE / metallo-exopeptidase / M17 aminopeptidase / Leucine Aminopeptidase / malaria / aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Macro domain-like
Similarity search - Domain/homology
CARBONATE ION / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMcGowan, S. / Suraweera, C. / Drinkwater, N.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1185354 Australia
CitationJournal: Mbio / Year: 2024
Title: Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties.
Authors: de Koning-Ward, T.F. / Drinkwater, N. / Edgar, R.C.S. / McGowan, S. / Scammells, P.J.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine aminopeptidase
B: Leucine aminopeptidase
C: Leucine aminopeptidase
D: Leucine aminopeptidase
E: Leucine aminopeptidase
F: Leucine aminopeptidase
G: Leucine aminopeptidase
H: Leucine aminopeptidase
I: Leucine aminopeptidase
J: Leucine aminopeptidase
K: Leucine aminopeptidase
L: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)713,38885
Polymers704,70012
Non-polymers8,68973
Water19,0241056
1
A: Leucine aminopeptidase
B: Leucine aminopeptidase
C: Leucine aminopeptidase
D: Leucine aminopeptidase
E: Leucine aminopeptidase
F: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,12344
Polymers352,3506
Non-polymers4,77338
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36450 Å2
ΔGint-750 kcal/mol
Surface area95210 Å2
MethodPISA
2
G: Leucine aminopeptidase
H: Leucine aminopeptidase
I: Leucine aminopeptidase
J: Leucine aminopeptidase
K: Leucine aminopeptidase
L: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,26641
Polymers352,3506
Non-polymers3,91635
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33620 Å2
ΔGint-705 kcal/mol
Surface area96920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.335, 176.725, 225.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Leucine aminopeptidase / PfLAP / M17 leucyl aminopeptidase / PfA-M17 / PfM17LAP


Mass: 58724.973 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: LAP, PF3D7_1446200 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IL11, leucyl aminopeptidase, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases

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Non-polymers , 5 types, 1129 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1056 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 10/11/2018 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→49.57 Å / Num. obs: 213083 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.983 / Rmerge(I) obs: 0.373 / Rpim(I) all: 0.152 / Rrim(I) all: 0.403 / Χ2: 0.95 / Net I/σ(I): 3.8 / Num. measured all: 1485932
Reflection shellResolution: 2.6→2.64 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 2.261 / Num. measured all: 72954 / Num. unique obs: 10487 / CC1/2: 0.575 / Rpim(I) all: 0.918 / Rrim(I) all: 2.442 / Χ2: 0.97 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.57 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 10830 5.1 %
Rwork0.2346 --
obs0.237 212389 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46583 0 368 1056 48007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247816
X-RAY DIFFRACTIONf_angle_d0.57564850
X-RAY DIFFRACTIONf_dihedral_angle_d9.2166646
X-RAY DIFFRACTIONf_chiral_restr0.0427493
X-RAY DIFFRACTIONf_plane_restr0.0038201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.3763710.31096630X-RAY DIFFRACTION100
2.63-2.660.35173360.31596711X-RAY DIFFRACTION100
2.66-2.690.34983550.31356637X-RAY DIFFRACTION100
2.69-2.730.36064110.30426641X-RAY DIFFRACTION100
2.73-2.760.36233360.30576677X-RAY DIFFRACTION100
2.76-2.80.32493710.28096651X-RAY DIFFRACTION100
2.8-2.840.3373300.28386726X-RAY DIFFRACTION100
2.84-2.880.33353550.28746654X-RAY DIFFRACTION100
2.88-2.930.34484140.27886648X-RAY DIFFRACTION100
2.93-2.980.34273980.28316616X-RAY DIFFRACTION100
2.98-3.030.33743440.28616752X-RAY DIFFRACTION100
3.03-3.080.3613490.29186670X-RAY DIFFRACTION100
3.08-3.140.37244140.29376657X-RAY DIFFRACTION100
3.14-3.210.3223520.27976683X-RAY DIFFRACTION100
3.21-3.280.32764020.26646674X-RAY DIFFRACTION100
3.28-3.350.29282980.24366767X-RAY DIFFRACTION100
3.35-3.440.31063360.24546690X-RAY DIFFRACTION100
3.44-3.530.31183820.24416696X-RAY DIFFRACTION100
3.53-3.630.28423690.24076704X-RAY DIFFRACTION100
3.63-3.750.28133570.22166717X-RAY DIFFRACTION100
3.75-3.880.24913700.21796708X-RAY DIFFRACTION100
3.88-4.040.26013290.20436760X-RAY DIFFRACTION100
4.04-4.220.22374000.20196682X-RAY DIFFRACTION100
4.22-4.450.22273560.18486764X-RAY DIFFRACTION100
4.45-4.720.22293400.17836789X-RAY DIFFRACTION100
4.72-5.090.22293710.1836789X-RAY DIFFRACTION100
5.09-5.60.25353060.20696860X-RAY DIFFRACTION100
5.6-6.410.24933170.21796891X-RAY DIFFRACTION100
6.41-8.070.22963790.20146883X-RAY DIFFRACTION100
8.07-49.570.1993820.18766832X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 89.6164 Å / Origin y: 56.0613 Å / Origin z: 78.2753 Å
111213212223313233
T0.3008 Å20.0041 Å20.0102 Å2-0.2337 Å20.0318 Å2--0.4309 Å2
L0.0501 °2-0.0074 °2-0.0101 °2-0.0181 °2-0.0008 °2--0.1486 °2
S-0.0025 Å °-0.0192 Å °0.2527 Å °0.0034 Å °0.0194 Å °-0.0314 Å °0.0061 Å °0.0023 Å °-0.0074 Å °
Refinement TLS groupSelection details: all

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