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- PDB-7tbb: Crystal structure of Plasmepsin X from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 7tbb
TitleCrystal structure of Plasmepsin X from Plasmodium falciparum
ComponentsPlasmepsin 10
KeywordsHYDROLASE / Aspartyl Protease
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / transport vesicle / protein processing / aspartic-type endopeptidase activity
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
ACETATE ION / Plasmepsin X
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChristensen, J.B. / Hodder, A.N. / Dietrich, M.H. / Scally, S.W. / Cowman, A.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust109662/Z/15/Z, 202749/Z/16/Z United Kingdom
CitationJournal: Structure / Year: 2022
Title: Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax.
Authors: Hodder, A.N. / Christensen, J. / Scally, S. / Triglia, T. / Ngo, A. / Birkinshaw, R.W. / Bailey, B. / Favuzza, P. / Dietrich, M.H. / Tham, W.H. / Czabotar, P.E. / Lowes, K. / Guo, Z. / ...Authors: Hodder, A.N. / Christensen, J. / Scally, S. / Triglia, T. / Ngo, A. / Birkinshaw, R.W. / Bailey, B. / Favuzza, P. / Dietrich, M.H. / Tham, W.H. / Czabotar, P.E. / Lowes, K. / Guo, Z. / Murgolo, N. / Lera Ruiz, M. / McCauley, J.A. / Sleebs, B.E. / Olsen, D. / Cowman, A.F.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasmepsin 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,73411
Polymers42,9491
Non-polymers78610
Water2,720151
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)62.308, 63.152, 79.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Plasmepsin 10


Mass: 42948.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2KNW6
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.82 Å3/Da / Density % sol: 32.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 25% (w/v) PEG1500, 10% (w/v) SPG pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.85→33.59 Å / Num. obs: 27357 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 30.85 Å2 / CC1/2: 1 / Rpim(I) all: 0.029 / Net I/σ(I): 15.71
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 2688 / CC1/2: 0.788 / Rpim(I) all: 0.0406 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UX4

5ux4


Resolution: 1.85→33.59 Å / SU ML: 0.2672 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2599 1995 7.3 %
Rwork0.2078 25339 -
obs0.2116 27334 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.97 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 52 151 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712725
X-RAY DIFFRACTIONf_angle_d0.94573679
X-RAY DIFFRACTIONf_chiral_restr0.0807408
X-RAY DIFFRACTIONf_plane_restr0.0073473
X-RAY DIFFRACTIONf_dihedral_angle_d15.9864986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.42591390.38731766X-RAY DIFFRACTION99.84
1.9-1.950.34441410.32071780X-RAY DIFFRACTION99.95
1.95-20.33251390.26971768X-RAY DIFFRACTION99.79
2-2.070.30181410.23541783X-RAY DIFFRACTION99.79
2.07-2.140.26421420.22621804X-RAY DIFFRACTION100
2.14-2.230.28911400.22491771X-RAY DIFFRACTION99.9
2.23-2.330.27751430.21741811X-RAY DIFFRACTION99.74
2.33-2.450.29551400.21311784X-RAY DIFFRACTION99.9
2.45-2.610.27031430.21191805X-RAY DIFFRACTION99.95
2.61-2.810.2681410.21561803X-RAY DIFFRACTION100
2.81-3.090.29311430.21391818X-RAY DIFFRACTION99.95
3.09-3.540.2461450.20321838X-RAY DIFFRACTION99.95
3.54-4.450.21161460.17491857X-RAY DIFFRACTION100
4.46-33.590.23961520.18981951X-RAY DIFFRACTION99.86

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