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- PDB-3fnt: Crystal structure of pepstatin A bound histo-aspartic protease (H... -

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Basic information

Entry
Database: PDB / ID: 3fnt
TitleCrystal structure of pepstatin A bound histo-aspartic protease (HAP) from Plasmodium falciparum
Components
  • HAP protein
  • Inhibitor, (IVA)VV(STA)A(STA)Enzyme inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Histo-aspartic protease / HAP / Plasmepsin / Pepstatin A / Aspartic protease / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


MHC class II antigen presentation / plasmepsin II / acquisition of nutrients from host / Neutrophil degranulation / vacuolar lumen / food vacuole / 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 domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pepstatin / Plasmepsin III
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 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: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAP protein
I: Inhibitor, (IVA)VV(STA)A(STA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2454
Polymers38,1212
Non-polymers1242
Water1629
1
A: HAP protein
I: Inhibitor, (IVA)VV(STA)A(STA)
hetero molecules

A: HAP protein
I: Inhibitor, (IVA)VV(STA)A(STA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4918
Polymers76,2424
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4740 Å2
ΔGint-38 kcal/mol
Surface area29400 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.7, 70.7, 158.7
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsOne molecule of histo-aspartic protease (HAP) is present in the asymmetric unit. One pepstatin A molecule is bound to the active site of the enzyme

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Components

#1: Protein HAP protein


Mass: 37435.250 Da / Num. of mol.: 1 / Fragment: Histo-aspartic protease (HAP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: HAP, PF14_0078 / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3)pLysS / References: UniProt: Q8IM15
#2: Protein/peptide Inhibitor, (IVA)VV(STA)A(STA) / Enzyme inhibitor /


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: unspecified
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 20000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. all: 7374 / Num. obs: 7350 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.2
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.2 / Num. unique all: 631 / % possible all: 99.5

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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: 1SME

1sme


Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.865 / SU B: 113.939 / SU ML: 0.84 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.732 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.353 366 5 %RANDOM
Rwork0.285 ---
obs0.288 6939 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: 66.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 8 9 2635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222690
X-RAY DIFFRACTIONr_angle_refined_deg2.2531.9843649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2145322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.11525.556117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.35615451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.072153
X-RAY DIFFRACTIONr_chiral_restr0.1280.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212014
X-RAY DIFFRACTIONr_mcbond_it0.9021.51612
X-RAY DIFFRACTIONr_mcangle_it1.7122629
X-RAY DIFFRACTIONr_scbond_it2.00731078
X-RAY DIFFRACTIONr_scangle_it3.6134.51020
LS refinement shellResolution: 3.3→3.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 26 -
Rwork0.45 492 -
obs--100 %
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)
12.6238-1.0982-0.95512.4868-0.51541.80970.04720.13880.2183-0.1131-0.01750.2229-0.3612-0.3921-0.02970.13230.0493-0.03920.35710.0060.1418-33.3032.9255.812
27.0662-0.359-0.91896.14290.30326.2190.1513-0.9266-0.07020.9243-0.3093-0.2010.52270.28090.1579-0.016-0.02270.03520.02860.0423-0.0501-15.553-8.80911.479
Refinement TLS group
IDEnd label asym-IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1AX-RAY DIFFRACTION1A2 - 210
2AX-RAY DIFFRACTION2A211 - 326

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