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- PDB-3s5k: Crystal structures of falcilysin, a M16 metalloprotease from the ... -

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Basic information

Entry
Database: PDB / ID: 3s5k
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: 3.2 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)139,1162
Polymers139,0501
Non-polymers651
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.780, 105.290, 114.760
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 20% PEG6000, 0.1M MES, 5 M Zn acetate,0.1% - mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 10, 2006
RadiationMonochromator: 0.9184 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.2→43.4 Å / Num. obs: 36165 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 3.3
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.autoMR:1.6_289)model building
PHENIX(phenix.refine: 1.6_289)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FGE

2fge


Resolution: 3.2→42.83 Å / SU ML: 0.54 / Isotropic thermal model: isotropic / σ(F): 1.14 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.316 2139 5.91 %
Rwork0.21 --
obs0.216 36165 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.52 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.8147 Å20 Å20 Å2
2--2.4692 Å2-0 Å2
3---4.3455 Å2
Refinement stepCycle: LAST / Resolution: 3.2→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8674 0 1 66 8741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018902
X-RAY DIFFRACTIONf_angle_d1.2911991
X-RAY DIFFRACTIONf_dihedral_angle_d22.2143304
X-RAY DIFFRACTIONf_chiral_restr0.0821313
X-RAY DIFFRACTIONf_plane_restr0.0041530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.31440.36382100.28023404X-RAY DIFFRACTION100
3.3144-3.4470.36752620.2783351X-RAY DIFFRACTION100
3.447-3.60380.33651900.23293423X-RAY DIFFRACTION100
3.6038-3.79370.33762270.21753412X-RAY DIFFRACTION100
3.7937-4.03130.33621990.21683386X-RAY DIFFRACTION100
4.0313-4.34220.28342100.18543417X-RAY DIFFRACTION100
4.3422-4.77870.26672090.16273437X-RAY DIFFRACTION100
4.7787-5.4690.33192210.18473376X-RAY DIFFRACTION100
5.469-6.88570.30282290.20943382X-RAY DIFFRACTION100
6.8857-42.83820.23511820.15743438X-RAY DIFFRACTION100

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