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- PDB-3fns: Crystal structure of histo-aspartic protease (HAP) from Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 3fns
TitleCrystal structure of histo-aspartic protease (HAP) from Plasmodium Falciparum
ComponentsHAP protein
KeywordsHYDROLASE / Histo-aspartic protease / HAP / Plasmepsin / Aspartic protease / HORMONE
Function / homology
Function and homology information


MHC class II antigen presentation / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / Neutrophil degranulation / food vacuole / aspartic-type endopeptidase activity / lysosome / 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 domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBhaumik, P. / Gustchina, A. / Wlodawer, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum.
Authors: Bhaumik, P. / Xiao, H. / Parr, C.L. / Kiso, Y. / Gustchina, A. / Yada, R.Y. / Wlodawer, A.
History
DepositionDec 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAP protein
B: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2638
Polymers74,8712
Non-polymers3926
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-209 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.800, 89.800, 198.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 0 - 326 / Label seq-ID: 6 - 330

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTwo molecules of histo-aspartic protease (HAP) are present in the asymmetric unit. Two molecules form a tight dimer related by a non-crystallographic symmetry.

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Components

#1: Protein HAP protein


Mass: 37435.250 Da / Num. of mol.: 2 / Fragment: Histo-aspartic protease (HAP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: HAP, PF14_0078 / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3)pLysS / References: UniProt: Q8IM15
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.02 %
Description: AUTHORS STATE THAT THE VALUE OF RMERGE IN THE HIGHEST RESOLUTION SHELL IS HIGH DUE TO POORLY DIFFRACTING CRYSTAL/HIGH SYMMETRY SPACE GROUP/ HIGHLY REDUNDANT DATA. CRYSTAL HAS SUFFERED SOME RADIATION DAMAGE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG 3000, 0.2M Zinc acetate, 0.1M sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 28973 / Num. obs: 28895 / % possible obs: 99.7 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3120 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
MrBUMPphasing
REFMAC5.4.0057refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANL

2anl


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.239 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.5 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 866 3 %RANDOM
Rwork0.225 ---
obs0.226 28018 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 6 104 5292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225316
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9647218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.045648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29625.546238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.42915908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.644156
X-RAY DIFFRACTIONr_chiral_restr0.1090.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214008
X-RAY DIFFRACTIONr_mcbond_it0.7781.53244
X-RAY DIFFRACTIONr_mcangle_it1.47725290
X-RAY DIFFRACTIONr_scbond_it1.74732072
X-RAY DIFFRACTIONr_scangle_it3.0044.51928
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2591 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.290.5
medium thermal1.092
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 62 -
Rwork0.299 2013 -
obs--100 %

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