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- PDB-8wxw: Falcilysin in complex with hemoglobin alpha chain peptide -

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Basic information

Entry
Database: PDB / ID: 8wxw
TitleFalcilysin in complex with hemoglobin alpha chain peptide
Components
  • Falcilysin
  • Hemoglobin subunit alpha fragment
KeywordsHYDROLASE / falcilysin-substrate complex / inactive mutant
Function / homology
Function and homology information


hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / nitric oxide transport / cellular oxidant detoxification / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex ...hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / nitric oxide transport / cellular oxidant detoxification / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / protein processing / metalloendopeptidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Peptidase M16C associated / Peptidase M16C associated / Peptidase M16C associated / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / : / Hemoglobin, pi ...Peptidase M16C associated / Peptidase M16C associated / Peptidase M16C associated / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / : / Hemoglobin, pi / Hemoglobin, alpha-type / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit alpha / Falcilysin
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLin, J.Q. / Lescar, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Falcilysin in complex with hemoglobin alpha chain peptide
Authors: Lin, J.Q. / Lescar, J.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Falcilysin
P: Hemoglobin subunit alpha fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,45014
Polymers136,7412
Non-polymers70912
Water13,727762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-106 kcal/mol
Surface area42890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.120, 105.720, 125.360
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 / Protein/peptide , 2 types, 2 molecules AP

#1: Protein Falcilysin


Mass: 135038.375 Da / Num. of mol.: 1 / Mutation: E132Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: FLN, PF3D7_1360800 / Production host: Escherichia coli (E. coli)
References: UniProt: Q76NL8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide Hemoglobin subunit alpha fragment


Mass: 1702.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P69905

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Non-polymers , 5 types, 774 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 4% w/v PEG 1500, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→48 Å / Num. obs: 104687 / % possible obs: 99.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 33 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08883 / Rpim(I) all: 0.02493 / Net I/σ(I): 19.1
Reflection shellResolution: 1.864→1.931 Å / Redundancy: 13.7 % / Num. unique obs: 10280 / CC1/2: 0.771 / CC star: 0.933 / % possible all: 99.17

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286-0000refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→46.09 Å / SU ML: 0.2455 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 22.9907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 10059 4.99 %
Rwork0.1889 191342 -
obs0.19 104647 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.72 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8916 0 35 762 9713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01019131
X-RAY DIFFRACTIONf_angle_d1.262412290
X-RAY DIFFRACTIONf_chiral_restr0.07171341
X-RAY DIFFRACTIONf_plane_restr0.00641566
X-RAY DIFFRACTIONf_dihedral_angle_d12.95473465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.890.43833270.39976170X-RAY DIFFRACTION96.31
1.89-1.910.32253360.32656374X-RAY DIFFRACTION99.94
1.91-1.930.35723400.30496390X-RAY DIFFRACTION99.97
1.93-1.960.3183330.2796380X-RAY DIFFRACTION100
1.96-1.980.27853350.26836374X-RAY DIFFRACTION99.96
1.98-2.010.28453350.25196387X-RAY DIFFRACTION99.96
2.01-2.040.25313360.24366364X-RAY DIFFRACTION99.97
2.04-2.070.27263390.22846390X-RAY DIFFRACTION99.97
2.07-2.10.23383330.2236390X-RAY DIFFRACTION100
2.1-2.130.24783370.22256407X-RAY DIFFRACTION100
2.13-2.170.2313340.21936369X-RAY DIFFRACTION100
2.17-2.210.23773360.2156405X-RAY DIFFRACTION99.97
2.21-2.250.25563320.21966424X-RAY DIFFRACTION100
2.25-2.30.24093330.21466351X-RAY DIFFRACTION100
2.3-2.350.23323360.20586391X-RAY DIFFRACTION99.97
2.35-2.40.20473280.20326397X-RAY DIFFRACTION100
2.4-2.460.23043400.20576349X-RAY DIFFRACTION100
2.46-2.530.23353420.26439X-RAY DIFFRACTION100
2.53-2.60.21833410.19966342X-RAY DIFFRACTION100
2.6-2.690.25623370.19776392X-RAY DIFFRACTION100
2.69-2.780.22633340.19536403X-RAY DIFFRACTION100
2.78-2.90.22223320.19536362X-RAY DIFFRACTION100
2.9-3.030.20833430.19966387X-RAY DIFFRACTION100
3.03-3.190.21283280.18536377X-RAY DIFFRACTION100
3.19-3.390.19233360.1786396X-RAY DIFFRACTION99.97
3.39-3.650.19833360.16176398X-RAY DIFFRACTION100
3.65-4.020.16743320.15726386X-RAY DIFFRACTION100
4.02-4.60.16363390.14556391X-RAY DIFFRACTION99.99
4.6-5.790.183330.16936374X-RAY DIFFRACTION100
5.79-46.090.18683360.17456383X-RAY DIFFRACTION99.93

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