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- PDB-3s5h: Crystal structures of falcilysin, a M16 metalloprotease from the ... -

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Basic information

Entry
Database: PDB / ID: 3s5h
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: 1.603 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 1.1Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Falcilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1092
Polymers139,0501
Non-polymers591
Water13,511750
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.540, 107.160, 128.860
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: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 11% PEG6000,10%PEG400,0.1M ADA, 20mM Mg acetate,20 mM Co acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2010 / Details: bent cylindrical mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.6→49.6 Å / Num. obs: 310281 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 3.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FGE

2fge


Resolution: 1.603→49.474 Å / SU ML: 0.26 / Isotropic thermal model: isotropic / σ(F): 0.12 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 6205 2 %
Rwork0.2271 --
obs0.2277 310281 93.57 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.15 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8605 Å20 Å20 Å2
2--0.7609 Å2-0 Å2
3---2.0996 Å2
Refinement stepCycle: LAST / Resolution: 1.603→49.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8854 0 1 750 9605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0169127
X-RAY DIFFRACTIONf_angle_d1.57812314
X-RAY DIFFRACTIONf_dihedral_angle_d15.0833477
X-RAY DIFFRACTIONf_chiral_restr0.1591352
X-RAY DIFFRACTIONf_plane_restr0.0081572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6033-1.66070.30696300.275330871X-RAY DIFFRACTION95
1.6607-1.72720.27556630.24132453X-RAY DIFFRACTION100
1.7272-1.80580.29036570.231232465X-RAY DIFFRACTION100
1.8058-1.9010.32966390.268331154X-RAY DIFFRACTION96
1.901-2.02010.54784710.51723009X-RAY DIFFRACTION71
2.0201-2.1760.25866540.20932050X-RAY DIFFRACTION99
2.176-2.3950.30955150.281425251X-RAY DIFFRACTION78
2.395-2.74160.2096670.178532513X-RAY DIFFRACTION100
2.7416-3.4540.246600.19332459X-RAY DIFFRACTION100
3.454-49.49720.18526490.178531851X-RAY DIFFRACTION98

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