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- PDB-7vpe: Falcilysin in complex with A1 -

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Basic information

Entry
Database: PDB / ID: 7vpe
TitleFalcilysin in complex with A1
ComponentsFalcilysin
KeywordsPROTEIN BINDING / Falcilysin / A1 / protease-inhibitor complex
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
Chem-7TU / ACETATE ION / Falcilysin
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLin, J.Q. / El Sahili, A. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: To Be Published
Title: Title is not available yet as we are preparing the manuscript. Will update again once the paper is out.
Authors: Lin, J.Q. / Lescar, J.
History
DepositionOct 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Falcilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,94611
Polymers135,0391
Non-polymers90710
Water19,0421057
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-34 kcal/mol
Surface area43380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.663, 106.157, 126.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Falcilysin


Mass: 135039.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: FLN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U7N7

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Non-polymers , 6 types, 1067 molecules

#2: Chemical ChemComp-7TU / (4S,5S)-1-[[3-[[(4S,5S)-4,5-diphenyl-4,5-dihydroimidazol-1-yl]methyl]phenyl]methyl]-4,5-diphenyl-4,5-dihydroimidazole


Mass: 546.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H34N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Morpheus G1 (0.1 M carboxylic acids, 0.1 M buffer system 1 pH 6.5, 10% w/v PEG 20,000, 20% v/v PEG 550mme)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.24 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 157897 / % possible obs: 99.57 % / Redundancy: 2 % / Biso Wilson estimate: 25.69 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.02663 / Rpim(I) all: 0.02663 / Rrim(I) all: 0.03765 / Net I/σ(I): 13.79
Reflection shellResolution: 1.624→1.682 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2978 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 15104 / CC1/2: 0.786 / CC star: 0.938 / Rpim(I) all: 0.2978 / Rrim(I) all: 0.4212 / % possible all: 95.96

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5H

3s5h


Resolution: 1.62→46.92 Å / SU ML: 0.2386 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 2000 1.27 %
Rwork0.1796 155876 -
obs0.1798 157876 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.62→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8847 0 54 1057 9958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00659081
X-RAY DIFFRACTIONf_angle_d0.865712230
X-RAY DIFFRACTIONf_chiral_restr0.05811334
X-RAY DIFFRACTIONf_plane_restr0.00481560
X-RAY DIFFRACTIONf_dihedral_angle_d17.15673474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.40221340.34510476X-RAY DIFFRACTION94.73
1.66-1.710.30941420.276311024X-RAY DIFFRACTION99.53
1.71-1.760.25591420.232411062X-RAY DIFFRACTION100
1.76-1.820.23941420.200811063X-RAY DIFFRACTION100
1.82-1.880.23611420.190511109X-RAY DIFFRACTION99.98
1.88-1.960.20671430.183211114X-RAY DIFFRACTION99.99
1.96-2.050.22381420.18611121X-RAY DIFFRACTION100
2.05-2.150.21041440.18211147X-RAY DIFFRACTION99.98
2.15-2.290.19131430.179911145X-RAY DIFFRACTION99.98
2.29-2.470.18961430.182611192X-RAY DIFFRACTION99.99
2.47-2.710.18961440.182111182X-RAY DIFFRACTION99.98
2.71-3.110.18671440.185911233X-RAY DIFFRACTION100
3.11-3.910.18491460.16511340X-RAY DIFFRACTION99.99
3.91-46.920.1731490.161211668X-RAY DIFFRACTION99.82

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