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- PDB-7tbd: Crystal structure of Plasmepsin X from Plasmodium vivax in comple... -

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Basic information

Entry
Database: PDB / ID: 7tbd
TitleCrystal structure of Plasmepsin X from Plasmodium vivax in complex with WM382
ComponentsPlasmepsin X
KeywordsHYDROLASE / Aspartyl Protease
Function / homology
Function and homology information


pepsin A / aspartic-type endopeptidase activity / proteolysis
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 / (malaria parasite P. vivax) hypothetical protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsHodder, A.N. / Christensen, J.B. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmepsin X
B: Plasmepsin X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4328
Polymers85,2282
Non-polymers2,2046
Water4,216234
1
A: Plasmepsin X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7053
Polymers42,6141
Non-polymers1,0912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasmepsin X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7275
Polymers42,6141
Non-polymers1,1134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.021, 88.440, 230.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-781-

HOH

21B-789-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 189 through 196 or (resid 197...
d_2ens_1(chain "B" and (resid 189 through 252 or (resid 253...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAALAA3 - 347
d_12ens_1NAGNAGC
d_13ens_1LIGLIGE
d_21ens_1ALAALAF1 - 345
d_22ens_1NAGNAGI
d_23ens_1LIGLIGA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Plasmepsin X


Mass: 42613.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_010019000, PVP01_0112200, PVT01_010014800 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1G4H6I9, pepsin A

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 238 molecules

#4: 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.: 2 / Source method: obtained synthetically / Formula: C29H36N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 0.1 M sodium HEPES pH 7.5, 2% (v/v) PEG 400 and 1 mM Anderson-Evans polyoxotungstate

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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: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.22→38.63 Å / Num. obs: 41807 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Rpim(I) all: 0.047 / Net I/σ(I): 11.4
Reflection shellResolution: 2.22→2.29 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3792 / CC1/2: 0.807 / Rpim(I) all: 0.473 / % possible all: 100

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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: 2.22→38.63 Å / SU ML: 0.2846 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 2030 4.86 %
Rwork0.1959 39739 -
obs0.1982 41769 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.25 Å2
Refinement stepCycle: LAST / Resolution: 2.22→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5395 0 153 234 5782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735691
X-RAY DIFFRACTIONf_angle_d0.9327747
X-RAY DIFFRACTIONf_chiral_restr0.0656867
X-RAY DIFFRACTIONf_plane_restr0.00711015
X-RAY DIFFRACTIONf_dihedral_angle_d18.17152043
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.02548695238 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.30831280.26282820X-RAY DIFFRACTION99.7
2.28-2.340.30431550.25972774X-RAY DIFFRACTION99.83
2.34-2.410.34911360.25662826X-RAY DIFFRACTION99.9
2.41-2.480.33041410.25732773X-RAY DIFFRACTION99.62
2.48-2.570.34771190.24242858X-RAY DIFFRACTION99.9
2.57-2.680.28821540.23492797X-RAY DIFFRACTION99.93
2.68-2.80.26161540.22972780X-RAY DIFFRACTION99.93
2.8-2.940.29251670.22382837X-RAY DIFFRACTION100
2.94-3.130.25761410.20562791X-RAY DIFFRACTION99.97
3.13-3.370.25371630.20052835X-RAY DIFFRACTION99.87
3.37-3.710.24831510.18242849X-RAY DIFFRACTION99.93
3.71-4.250.20131430.15962857X-RAY DIFFRACTION100
4.25-5.350.19671330.14822913X-RAY DIFFRACTION100
5.35-38.630.21561450.20223029X-RAY DIFFRACTION99.84

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