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- PDB-7tbc: Crystal structure of Plasmepsin X from Plasmodium falciparum in c... -

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Basic information

Entry
Database: PDB / ID: 7tbc
TitleCrystal structure of Plasmepsin X from Plasmodium falciparum in complex with WM382
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
Chem-I0L / Plasmepsin X
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsChristensen, J.B. / Hodder, A.N. / 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 1.3Nov 6, 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)44,80019
Polymers42,9491
Non-polymers1,85118
Water1629
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)109.320, 109.320, 118.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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
#3: 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

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Non-polymers , 4 types, 26 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-I0L / (4R)-4-[(2E)-4,4-diethyl-2-imino-6-oxo-1,3-diazinan-1-yl]-N-[(4S)-2,2-dimethyl-3,4-dihydro-2H-1-benzopyran-4-yl]-3,4-dihydro-2H-1-benzopyran-6-carboxamide


Mass: 504.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4.75 Å3/Da / Density % sol: 74.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.1M bicine-tris pH 8.5, 2.85% (v/v) diethylene glycol, 6.35% (v/v) pentaethylene glycol, 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) polyethylene ...Details: 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.1M bicine-tris pH 8.5, 2.85% (v/v) diethylene glycol, 6.35% (v/v) pentaethylene glycol, 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) polyethylene glycol 3350, 5.2% (v/v) tetraethylene glycol, 4.1% (v/v) triethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.76→49.63 Å / Num. obs: 21289 / % possible obs: 99 % / Redundancy: 22.6 % / Biso Wilson estimate: 96.22 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 12.5
Reflection shellResolution: 2.76→2.91 Å / Redundancy: 6.5 % / Num. unique obs: 2860 / CC1/2: 0.936 / Rpim(I) all: 0.496 / % possible all: 93.6

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Processing

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

7tbb


Resolution: 2.76→49.62 Å / SU ML: 0.3746 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7843
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 1061 4.99 %
Rwork0.1966 20199 -
obs0.1982 21260 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.48 Å2
Refinement stepCycle: LAST / Resolution: 2.76→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 124 9 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252837
X-RAY DIFFRACTIONf_angle_d0.56133820
X-RAY DIFFRACTIONf_chiral_restr0.0489414
X-RAY DIFFRACTIONf_plane_restr0.0041501
X-RAY DIFFRACTIONf_dihedral_angle_d16.68851047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.880.3941240.31612293X-RAY DIFFRACTION91.59
2.88-3.040.25911280.23672518X-RAY DIFFRACTION99.51
3.04-3.230.31051270.27412525X-RAY DIFFRACTION99.96
3.23-3.480.26531380.19892504X-RAY DIFFRACTION99.96
3.48-3.820.23661350.21852539X-RAY DIFFRACTION99.96
3.83-4.380.23881380.18332561X-RAY DIFFRACTION100
4.38-5.510.20141340.17182564X-RAY DIFFRACTION100
5.52-49.620.20091370.192695X-RAY DIFFRACTION99.93

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