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- PDB-6kub: Crystal structure of Plasmodium falciparum histo-aspartic proteas... -

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Basic information

Entry
Database: PDB / ID: 6kub
TitleCrystal structure of Plasmodium falciparum histo-aspartic protease (HAP) zymogen (Form 1)
ComponentsHAP protein
KeywordsHYDROLASE / Histo-Aspartic protease / HAP / Plasmepsin / Proplasmepsin / Zymogen / Aspartic Protease
Function / homology
Function and homology information


plasmepsin II / acquisition of nutrients from host / 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
DI(HYDROXYETHYL)ETHER / Plasmepsin III
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRathore, I. / Mishra, V. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)Ramalingaswami re-entry fellowship India
CitationJournal: Febs J. / Year: 2021
Title: Activation mechanism of plasmepsins, pepsin-like aspartic proteases from Plasmodium, follows a unique trans-activation pathway.
Authors: Rathore, I. / Mishra, V. / Patel, C. / Xiao, H. / Gustchina, A. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P.
History
DepositionAug 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,92010
Polymers43,0491
Non-polymers8719
Water5,981332
1
A: HAP protein
hetero molecules

A: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,83920
Polymers86,0982
Non-polymers1,74218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5700 Å2
ΔGint-6 kcal/mol
Surface area33710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.900, 69.300, 73.400
Angle α, β, γ (deg.)90.000, 126.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

21A-815-

HOH

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Components

#1: Protein HAP protein / Histo-aspartic protease


Mass: 43048.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: hap / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y006
#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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium citrate tribasic pH 7.0, 0.1M Imidazole pH 7.0, 20% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→35.49 Å / Num. obs: 33708 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 1.102 / Num. unique obs: 4599 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0124refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QVC

3qvc


Resolution: 2→35.49 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 12.959 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.159
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1686 5 %RANDOM
Rwork0.1833 ---
obs0.1859 32021 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 237.67 Å2 / Biso mean: 60.408 Å2 / Biso min: 30.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.35 Å2
2--1.31 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 2→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 57 332 3426
Biso mean--81.79 63.99 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023221
X-RAY DIFFRACTIONr_bond_other_d0.0020.023068
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9784356
X-RAY DIFFRACTIONr_angle_other_deg0.963.0017130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3575399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99725.54139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77915570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.337154
X-RAY DIFFRACTIONr_chiral_restr0.10.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213557
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02699
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 126 -
Rwork0.403 2384 -
all-2510 -
obs--99.8 %
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)
16.1081-0.5673-0.51330.59090.38131.0443-0.00890.0337-0.38910.0041-0.02050.1355-0.0274-0.01810.02950.18780.0022-0.02710.16040.00280.11333.4601-6.572-23.4241
215.19034.7028-0.96894.16820.49960.3109-0.35290.6378-0.5011-0.59190.5353-0.681-0.1438-0.0018-0.18250.6647-0.13150.02820.62360.09350.259612.36639.575-27.0432
31.42260.23320.5920.9655-0.3091.8939-0.14470.05070.0152-0.20530.07910.12250.0234-0.20510.06560.1470.0203-0.11940.217-0.02390.1193-21.75043.1385-27.5604
42.0228-0.9379-0.03031.01450.71511.398-0.0445-0.01180.0097-0.15050.03580.0087-0.23540.09640.00870.1869-0.0196-0.070.17760.0140.03780.62017.1272-13.8549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 117P
2X-RAY DIFFRACTION2A118P - 9
3X-RAY DIFFRACTION3A10 - 186
4X-RAY DIFFRACTION4A187 - 328

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