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- PDB-3s5i: Crystal structures of falcilysin, a M16 metalloprotease from the ... -

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Basic information

Entry
Database: PDB / ID: 3s5i
TitleCrystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum
ComponentsFalcilysin
KeywordsHYDROLASE / M16 metalloprotease / peptidase
Function / homology
Function and homology information


hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / protein processing / metalloendopeptidase activity / metal ion binding
Similarity search - Function
: / Peptidase M16C associated / Peptidase M16C associated / PreP C-terminal domain / Peptidase M16C associated / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 Å
AuthorsMorgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T.
CitationJournal: To be Published
Title: Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum
Authors: Morgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Falcilysin


Theoretical massNumber of molelcules
Total (without water)139,0501
Polymers139,0501
Non-polymers00
Water28,3021571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.350, 107.120, 128.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Falcilysin


Mass: 139050.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: HB3 / Gene: flN, PF13_0322 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76NL8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1571 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.2
Details: 11% PEG6000, 10%PEG400, 0.1M ADA, 20mM Mg acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2010 / Details: Pt coated Si mirror
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.74→35.3 Å / Num. obs: 284102 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.1 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 15
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 4.8 / Num. unique all: 132487 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FGE

2fge


Resolution: 1.743→34.395 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 7724 3.02 %random
Rwork0.1557 ---
all0.1569 284102 --
obs0.1565 255661 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.443 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.7022 Å20 Å20 Å2
2--0.2368 Å2-0 Å2
3---0.4654 Å2
Refinement stepCycle: LAST / Resolution: 1.743→34.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8971 0 0 1571 10542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149411
X-RAY DIFFRACTIONf_angle_d1.40512747
X-RAY DIFFRACTIONf_dihedral_angle_d16.423591
X-RAY DIFFRACTIONf_chiral_restr0.1061399
X-RAY DIFFRACTIONf_plane_restr0.0071643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.743-1.80530.23278270.196124639X-RAY DIFFRACTION100
1.8053-1.87760.24217450.185924831X-RAY DIFFRACTION100
1.8776-1.9630.21758240.169124714X-RAY DIFFRACTION100
1.963-2.06650.20467730.155624812X-RAY DIFFRACTION100
2.0665-2.1960.20467990.147824761X-RAY DIFFRACTION100
2.196-2.36550.20237510.142624838X-RAY DIFFRACTION100
2.3655-2.60340.19236900.139124892X-RAY DIFFRACTION100
2.6034-2.980.18557820.143724801X-RAY DIFFRACTION100
2.98-3.75370.17767640.149724847X-RAY DIFFRACTION100
3.7537-34.40140.17917690.149524802X-RAY DIFFRACTION100

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