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- PDB-5jod: Structure of proplasmepsin IV from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 5jod
TitleStructure of proplasmepsin IV from Plasmodium falciparum
ComponentsProplasmepsin IV
KeywordsHYDROLASE / malaria
Function / homology
Function and homology information


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
Peptidase A1 domain-containing protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.528 Å
AuthorsRecacha, R. / Akopjana, I. / Tars, K. / Jaudzems, K.
Citation
Journal: Acta Crystallogr.,Sect.F / 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
DepositionMay 2, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionAug 17, 2016ID: 4y7h
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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: Proplasmepsin IV
B: Proplasmepsin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57411
Polymers84,7452
Non-polymers8299
Water12,412689
1
B: Proplasmepsin IV
hetero molecules

A: Proplasmepsin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57411
Polymers84,7452
Non-polymers8299
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,y-1/2,-z1
2
A: Proplasmepsin IV
hetero molecules

B: Proplasmepsin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,57411
Polymers84,7452
Non-polymers8299
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
Buried area4210 Å2
ΔGint-22 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.909, 62.780, 94.030
Angle α, β, γ (deg.)90.00, 113.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proplasmepsin IV


Mass: 42372.699 Da / Num. of mol.: 2 / Fragment: UNP residues 75-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFBG_05102 / Production host: Escherichia coli (E. coli) / References: UniProt: W7FF86
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 100 mM sodium citrate, 25% (w/v) PEG 3350 200 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twinOperator: -h,-k,h+l / Fraction: 0.04
ReflectionResolution: 1.53→48.41 Å / Num. obs: 129149 / % possible obs: 96.3 % / Redundancy: 2.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.065 / Net I/av σ(I): 7.5 / Net I/σ(I): 7.5
Reflection shellResolution: 1.53→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.2 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PFZ

1pfz


Resolution: 1.528→36.679 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 6475 5.02 %
Rwork0.1787 --
obs0.1802 129074 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.528→36.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 54 689 6723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076200
X-RAY DIFFRACTIONf_angle_d1.078387
X-RAY DIFFRACTIONf_dihedral_angle_d12.7072244
X-RAY DIFFRACTIONf_chiral_restr0.045910
X-RAY DIFFRACTIONf_plane_restr0.0051068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.528-1.54540.39572160.37223960X-RAY DIFFRACTION94
1.5454-1.56350.35382190.35034065X-RAY DIFFRACTION97
1.5635-1.58260.33782210.33344050X-RAY DIFFRACTION96
1.5826-1.60260.34322060.31874102X-RAY DIFFRACTION97
1.6026-1.62370.29651960.30244155X-RAY DIFFRACTION97
1.6237-1.6460.31782270.28124037X-RAY DIFFRACTION97
1.646-1.66950.30672150.27864097X-RAY DIFFRACTION97
1.6695-1.69440.28792360.26444101X-RAY DIFFRACTION97
1.6944-1.72090.29172100.25064068X-RAY DIFFRACTION97
1.7209-1.74910.27051970.23934133X-RAY DIFFRACTION97
1.7491-1.77930.24992250.23264049X-RAY DIFFRACTION97
1.7793-1.81160.2472300.21914127X-RAY DIFFRACTION97
1.8116-1.84650.23592240.20524117X-RAY DIFFRACTION97
1.8465-1.88410.22862180.19574092X-RAY DIFFRACTION97
1.8841-1.92510.24372130.19514076X-RAY DIFFRACTION97
1.9251-1.96990.222400.1844064X-RAY DIFFRACTION97
1.9699-2.01920.18162310.1714133X-RAY DIFFRACTION97
2.0192-2.07370.22042200.18214071X-RAY DIFFRACTION97
2.0737-2.13480.19682480.174092X-RAY DIFFRACTION97
2.1348-2.20370.19722190.16394107X-RAY DIFFRACTION97
2.2037-2.28240.17812180.16674095X-RAY DIFFRACTION97
2.2824-2.37380.1982020.16254127X-RAY DIFFRACTION97
2.3738-2.48180.20212120.16684127X-RAY DIFFRACTION97
2.4818-2.61260.20632120.17314118X-RAY DIFFRACTION97
2.6126-2.77620.18011950.17074119X-RAY DIFFRACTION96
2.7762-2.99050.2011980.17074111X-RAY DIFFRACTION96
2.9905-3.29130.21971970.1634126X-RAY DIFFRACTION96
3.2913-3.76710.18062270.1464093X-RAY DIFFRACTION95
3.7671-4.74450.15032040.12764041X-RAY DIFFRACTION94
4.7445-36.68920.18671990.16023946X-RAY DIFFRACTION89
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)
10.7176-0.0028-0.41621.3471-0.06540.8-0.02860.1297-0.0307-0.1282-0.00290.04760.0049-0.05760.02740.11970.0031-0.04120.1994-0.01490.13460.4164-8.717211.6585
20.70590.37440.09720.53990.24460.62070.04560.02440.0692-0.0438-0.03150.0291-0.0477-0.0069-0.01790.1360.0241-0.02030.15650.01520.20788.2049-16.299436.4994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:328)
2X-RAY DIFFRACTION2(chain B and resseq 1:328)

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