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- PDB-7t3v: Metal dependent activation of Plasmodium falciparum M17 aminopept... -

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Basic information

Entry
Database: PDB / ID: 7t3v
TitleMetal dependent activation of Plasmodium falciparum M17 aminopeptidase, spacegroup P22121 after crystals soaked with Zn2+
ComponentsM17 leucyl aminopeptidase
KeywordsHYDROLASE / Metallo aminopeptidase / malaria / PEPTIDE BINDING PROTEIN
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 / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like ...Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
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: 2.3 Å
AuthorsWebb, C.T. / McGowan, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase.
Authors: Webb, C.T. / Yang, W. / Riley, B.T. / Hayes, B.K. / Sivaraman, K.K. / Malcolm, T.R. / Harrop, S. / Atkinson, S.C. / Kass, I. / Buckle, A.M. / Drinkwater, N. / McGowan, S.
History
DepositionDec 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,04028
Polymers351,4676
Non-polymers1,57322
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.760, 172.756, 176.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.178559569819, 0.763135107483, 0.621080741734), (-0.780390900291, -0.494285304276, 0.382977911529), (0.599254973086, -0.416301388062, 0.683803064872)-24.1755427856, 65.1645682623, 13.6574323701
2given(-0.197441603477, -0.778105228149, 0.596296123703), (0.768623394429, -0.500419717572, -0.398494898089), (0.608469301406, 0.37964767903, 0.696873553131)38.6731918672, 56.2258625608, -18.9490365678
3given(-0.608244995586, 0.770606743589, -0.190271574544), (0.762365258636, 0.500423269675, -0.410336159255), (-0.220991488001, -0.394641353513, -0.891863758838)11.3822326584, 15.8323406847, 82.8129598208
4given(-0.604725336674, -0.77567121118, -0.180669420021), (-0.765171474468, 0.502907955187, 0.401990302458), (-0.220952216203, 0.381336807502, -0.897642666878)74.3550744484, 24.2159931778, 51.2822304828
5given(0.563394464992, 0.00158977850821, -0.826186510069), (0.001952755001, -0.99999791778, -0.00059260691493), (-0.826185731881, -0.00127946838351, -0.563396396329)36.4317781298, 81.0449852682, 69.9367899144

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
M17 leucyl aminopeptidase


Mass: 58577.777 Da / Num. of mol.: 6
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: Q8IL11, leucyl aminopeptidase

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Non-polymers , 5 types, 301 molecules

#2: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM HEPES pH 8.0, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→48.26 Å / Num. obs: 144874 / % possible obs: 95.49 % / Redundancy: 9.7 % / Biso Wilson estimate: 44.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1411 / Net I/σ(I): 11.81
Reflection shellResolution: 2.3→2.385 Å / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 14859 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SRV

7srv


Resolution: 2.3→47.24 Å / SU ML: 0.3574 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.6706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 1994 1.38 %
Rwork0.219 142754 -
obs0.2196 144748 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23167 0 62 279 23508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003923668
X-RAY DIFFRACTIONf_angle_d0.595232189
X-RAY DIFFRACTIONf_chiral_restr0.04453756
X-RAY DIFFRACTIONf_plane_restr0.00394093
X-RAY DIFFRACTIONf_dihedral_angle_d5.7643295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.42421490.399810440X-RAY DIFFRACTION98.74
2.36-2.420.37611460.365810570X-RAY DIFFRACTION99.8
2.42-2.50.38041480.342410541X-RAY DIFFRACTION99.87
2.5-2.580.4381450.325210565X-RAY DIFFRACTION99.93
2.58-2.650.37011130.3087817X-RAY DIFFRACTION97.23
2.7-2.780.3687920.28096883X-RAY DIFFRACTION97.8
2.78-2.90.3151560.268710624X-RAY DIFFRACTION99.98
2.9-3.050.29821470.254510616X-RAY DIFFRACTION99.92
3.05-3.250.33741440.250810622X-RAY DIFFRACTION99.97
3.25-3.50.321460.230810682X-RAY DIFFRACTION99.92
3.5-3.850.23971520.19810695X-RAY DIFFRACTION99.98
3.85-4.40.1871500.16910735X-RAY DIFFRACTION99.99
4.4-5.550.20041500.159910838X-RAY DIFFRACTION100
5.55-47.240.20421560.183111126X-RAY DIFFRACTION99.7

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