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- PDB-5bwy: Structure of proplasmepsin II from Plasmodium falciparum, Space G... -

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Basic information

Entry
Database: PDB / ID: 5bwy
TitleStructure of proplasmepsin II from Plasmodium falciparum, Space Group P43212
ComponentsPlasmepsin-2
KeywordsHYDROLASE / malaria
Function / homology
Function and homology information


cytostome / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Plasmepsin II / Plasmepsin-2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.644 Å
AuthorsRecacha, R. / Akopjana, I. / Tars, K. / Jaudzems, K.
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins.
Authors: Recacha, R. / Jaudzems, K. / Akopjana, I. / Jirgensons, A. / Tars, K.
#1: Journal: Nat. Struct. Biol. / Year: 1999
Title: Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from plasmodium falciparum.
Authors: Bernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N.
#2: Journal: J. Mol. Biol. / Year: 2003
Title: Structural insights into the activation of P. vivax plasmepsin.
Authors: Bernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasmepsin-2


Theoretical massNumber of molelcules
Total (without water)42,3751
Polymers42,3751
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.380, 89.380, 115.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Plasmepsin-2 /


Mass: 42374.969 Da / Num. of mol.: 1 / Fragment: UNP residues 78-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFAG_05140 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / References: UniProt: W7FL77, UniProt: P46925*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium Citrate, 0.1 M Sodium Acetate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: May 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.64→44.7 Å / Num. all: 14252 / Num. obs: 14252 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2.64→2.76 Å / Redundancy: 5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PFZ

1pfz


Resolution: 2.644→44.69 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 752 5.28 %
Rwork0.2038 --
obs0.2059 14249 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.644→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 0 51 3036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033102
X-RAY DIFFRACTIONf_angle_d0.7644222
X-RAY DIFFRACTIONf_dihedral_angle_d15.3531125
X-RAY DIFFRACTIONf_chiral_restr0.029477
X-RAY DIFFRACTIONf_plane_restr0.003541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6441-2.84820.35091510.3292621X-RAY DIFFRACTION100
2.8482-3.13480.32451490.26322645X-RAY DIFFRACTION100
3.1348-3.58820.28531440.21362673X-RAY DIFFRACTION100
3.5882-4.52010.23871540.17412704X-RAY DIFFRACTION100
4.5201-44.69640.17441540.1712854X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.22280.3401-1.08663.11620.2347.74280.3010.3262-0.1451-0.7867-0.0834-0.3578-0.55630.6991-0.25290.6463-0.07260.04260.5691-0.10120.4624-9.5595-4.198419.8573
22.7415-0.85240.36574.0514-2.21013.8918-0.09030.1804-0.1425-0.21560.1359-0.01530.48940.4182-0.01880.4816-0.06420.01430.3312-0.07040.2607-17.5022-11.680638.9101
34.179-1.2632-1.33512.56610.99996.59710.1930.68370.0378-1.11930.05230.2835-0.5272-0.4053-0.26890.8564-0.0448-0.13640.38740.02080.385-24.9271-0.359717.3616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 78P through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 329 )

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