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- PDB-1pfz: PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM -

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Basic information

Entry
Database: PDB / ID: 1pfz
TitlePROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM
ComponentsPROPLASMEPSIN II
KeywordsASPARTIC PROTEASE ZYMOGEN / ASPARTIC PROTEINASE ZYMOGEN / HEMOGLOBINASE / MALARIA / HYDROLASE / ASPARTYL PROTEASE / GLYCOPROTEIN
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
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
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N.G.
Citation
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.
#1: Journal: FEBS Lett. / Year: 1994
Title: High Level Expression and Characterisation of Plasmepsin II, an Aspartic Proteinase from Plasmodium Falciparum
Authors: Hill, J. / Tyas, L. / Phylip, L.H. / Kay, J. / Dunn, B.M. / Berry, C.
History
DepositionJul 7, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROPLASMEPSIN II
B: PROPLASMEPSIN II
C: PROPLASMEPSIN II
D: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,48610
Polymers170,9334
Non-polymers5536
Water13,169731
1
A: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0104
Polymers42,7331
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROPLASMEPSIN II


Theoretical massNumber of molelcules
Total (without water)42,7331
Polymers42,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8252
Polymers42,7331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9183
Polymers42,7331
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: PROPLASMEPSIN II
D: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5593
Polymers85,4672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-16 kcal/mol
Surface area31330 Å2
MethodPISA
6
A: PROPLASMEPSIN II
C: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9277
Polymers85,4672
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-19 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.007, 133.223, 114.234
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999952, 0.002348, 0.009486), (0.002185, -0.999849, 0.017241), (0.009525, -0.01722, -0.999806)-26.9129, 31.2322, 146.6722
2given(-0.999873, -0.009973, -0.012427), (-0.009592, 0.999495, -0.030297), (0.012723, -0.030174, -0.999464)8.1204, 3.9222, 158.36391
3given(-0.999616, -0.027342, -0.004556), (0.027681, -0.976002, -0.215994), (0.001459, -0.216037, 0.976384)32.1287, 45.2125, 17.1313

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Components

#1: Protein
PROPLASMEPSIN II


Mass: 42733.336 Da / Num. of mol.: 4
Mutation: 76 RESIDUES AT THE N-TERMINUS OF THE PROSEGMENT (1P - 76P) HAVE BEEN TRUNCATED, 3 RESIDUES (GLY-ARG-GLY) HAVE BEEN ADDED AT THE N-TERMINUS AS AN ARTIFACT OF THE EXPRESSION SYSTEM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Cell line: BL21 / Organelle: DIGESTIVE VACUOLE / Plasmid: PBLUESCRIPT KS+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P46925, plasmepsin II
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNOMENCLATURE: THE PROSEGMENT RESIDUES HAVE INSERTION CODE P (78/79 P - 118/124 P). NUMBERING FOR ...NOMENCLATURE: THE PROSEGMENT RESIDUES HAVE INSERTION CODE P (78/79 P - 118/124 P). NUMBERING FOR THE MATURE SEGMENT CORRESPONDS TO P. FALCIPARUM PLASMEPSIN II, PDB ENTRY 1SME.

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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: 2.5 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 105 K / Method: vapor diffusion, sitting drop
Details: 2 microlitter of protein splution was mixed with 7 microlitter of reservoir solution
PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 mg/mlprotein1drop
225 %PEG40001reservoir
30.18 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir
50.1 %beta-octylglucoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 114943 / % possible obs: 96.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3 / % possible all: 91.5
Reflection shell
*PLUS
% possible obs: 91.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3refinement
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2505951.19 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED DATA CUTOFF HIGH (ABS(F)) : 2505951.19 DATA CUTOFF LOW (ABS(F)) : 0.000000
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2699 2.1 %RANDOM
Rwork0.214 ---
obs0.214 125751 96.1 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å2-0.11 Å2
2---5.19 Å20 Å2
3---2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11648 0 36 731 12415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 419 2.1 %
Rwork0.276 19202 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMGLR.TOP
X-RAY DIFFRACTION3GLR.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Rfactor obs: 0.276

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