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- PDB-8svl: Plasmodium falciparum M1 aminopeptidase bound to MMV1557817 -

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Basic information

Entry
Database: PDB / ID: 8svl
TitlePlasmodium falciparum M1 aminopeptidase bound to MMV1557817
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE / metallo-exopeptidase / protease inhibitor / malaria / Plasmodium / M1 aminopeptidase
Function / homology
Function and homology information


symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm
Similarity search - Function
Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase ...Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
: / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.504 Å
AuthorsMcGowan, S. / 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

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Assembly

Deposited unit
A: M1 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,41416
Polymers127,0961
Non-polymers1,31815
Water23,1311284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.899, 109.010, 118.030
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, 1 molecules A

#1: Protein M1 family aminopeptidase / Pfa-M1


Mass: 127095.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli)
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 1299 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-WRC / N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide


Mass: 394.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21F3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1284 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.9 Å3/Da / Density % sol: 35.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris pH 8.5, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→44.07 Å / Num. obs: 153480 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Net I/σ(I): 11.5 / Num. measured all: 1055651
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 1.599 / Num. measured all: 47886 / Num. unique obs: 7492 / CC1/2: 0.431 / Rpim(I) all: 0.685 / Rrim(I) all: 1.742 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.504→42.658 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 7575 4.94 %
Rwork0.155 --
obs0.1567 153369 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.504→42.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 82 1284 8590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0197561
X-RAY DIFFRACTIONf_angle_d1.70310256
X-RAY DIFFRACTIONf_dihedral_angle_d13.5962852
X-RAY DIFFRACTIONf_chiral_restr0.0941129
X-RAY DIFFRACTIONf_plane_restr0.0111310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.504-1.52110.29212330.28614772X-RAY DIFFRACTION100
1.5211-1.5390.29522350.27074855X-RAY DIFFRACTION100
1.539-1.55780.29122370.26174861X-RAY DIFFRACTION100
1.5578-1.57750.30012540.2524752X-RAY DIFFRACTION100
1.5775-1.59820.25712550.2424815X-RAY DIFFRACTION100
1.5982-1.62010.25132440.22714802X-RAY DIFFRACTION100
1.6201-1.64330.31362290.23474861X-RAY DIFFRACTION100
1.6433-1.66780.27692560.22384813X-RAY DIFFRACTION100
1.6678-1.69390.24452690.20594795X-RAY DIFFRACTION100
1.6939-1.72160.27122560.20484805X-RAY DIFFRACTION100
1.7216-1.75130.2582190.19134853X-RAY DIFFRACTION100
1.7513-1.78320.21562470.17864861X-RAY DIFFRACTION100
1.7832-1.81750.20092270.17494859X-RAY DIFFRACTION100
1.8175-1.85460.2252410.16734790X-RAY DIFFRACTION100
1.8546-1.89490.20282450.1584853X-RAY DIFFRACTION100
1.8949-1.9390.20232640.15754831X-RAY DIFFRACTION100
1.939-1.98750.19392530.15694846X-RAY DIFFRACTION100
1.9875-2.04120.17822480.15344833X-RAY DIFFRACTION100
2.0412-2.10130.18482920.14414836X-RAY DIFFRACTION100
2.1013-2.16910.17282700.14174819X-RAY DIFFRACTION100
2.1691-2.24660.18992430.13854862X-RAY DIFFRACTION100
2.2466-2.33650.18062620.14294880X-RAY DIFFRACTION100
2.3365-2.44290.18962400.14524868X-RAY DIFFRACTION100
2.4429-2.57160.19232820.14664848X-RAY DIFFRACTION100
2.5716-2.73270.19162560.14894891X-RAY DIFFRACTION100
2.7327-2.94370.19712630.1484903X-RAY DIFFRACTION100
2.9437-3.23980.18332540.14134922X-RAY DIFFRACTION100
3.2398-3.70840.13972500.12864960X-RAY DIFFRACTION100
3.7084-4.67130.14522540.11835004X-RAY DIFFRACTION100
4.6713-42.6580.15732970.14475144X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.7422 Å / Origin y: 4.1459 Å / Origin z: 10.2788 Å
111213212223313233
T0.082 Å2-0.0041 Å20.0058 Å2-0.1047 Å20.01 Å2--0.0895 Å2
L0.3746 °2-0.1393 °20.0038 °2-0.7476 °20.1398 °2--0.5832 °2
S-0.0456 Å °-0.0076 Å °0.0287 Å °0.0132 Å °0.0045 Å °-0.0148 Å °-0.0256 Å °-0.0044 Å °0.0399 Å °
Refinement TLS groupSelection details: all

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