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

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Basic information

Entry
Database: PDB / ID: 6kuc
TitleCrystal structure of Plasmodium falciparum histo-aspartic protease (HAP) zymogen (Form 2)
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: 2.5 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

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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)43,93410
Polymers43,0491
Non-polymers8859
Water2,108117
1
A: HAP protein
hetero molecules

A: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,86720
Polymers86,0982
Non-polymers1,77018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5290 Å2
ΔGint3 kcal/mol
Surface area34460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.700, 70.000, 73.000
Angle α, β, γ (deg.)90.000, 126.100, 90.000
Int Tables number5
Space group name H-MC121

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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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v Polyethylene glycol 3350

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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: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→36.5 Å / Num. obs: 17267 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.12
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1890

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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 / Resolution: 2.5→36.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 28.288 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.46 / ESU R Free: 0.28
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 864 5 %RANDOM
Rwork0.1918 ---
obs0.1947 16407 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.62 Å2 / Biso mean: 63.264 Å2 / Biso min: 31.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.05 Å2
2--0.27 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 2.5→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 58 117 3193
Biso mean--102.03 60.74 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023146
X-RAY DIFFRACTIONr_bond_other_d0.0060.022987
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9774240
X-RAY DIFFRACTIONr_angle_other_deg1.0936931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7545378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32825.474137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.03715549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.477154
X-RAY DIFFRACTIONr_chiral_restr0.1180.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213451
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02685
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 62 -
Rwork0.39 1178 -
all-1240 -
obs--98.02 %
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)
18.5566-0.4621-0.4620.5330.06680.11320.0089-0.2382-0.33090.0866-0.02630.1193-0.04310.01840.01750.2862-0.0083-0.01670.37710.00880.189244.3717-6.15655.589
20.0863-0.2612-0.31960.88981.05131.2677-0.013-0.00440.11770.06660.3644-0.41960.12770.3485-0.35140.8227-0.0783-0.12771.30650.28731.346757.71689.4563.9339
31.8220.7041.32841.033-0.03013.3416-0.32960.04560.1321-0.26880.06490.1816-0.2646-0.31040.26470.22320.0624-0.1640.401-0.05510.143919.25554.47332.478
42.2738-0.83530.07381.20340.65121.8681-0.04030.0409-0.1108-0.2235-0.02150.0527-0.41950.17570.06190.2755-0.0497-0.09570.44830.01540.049841.60266.580715.893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 117P
2X-RAY DIFFRACTION2A118P - 4
3X-RAY DIFFRACTION3A5 - 196
4X-RAY DIFFRACTION4A197 - 328

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