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- PDB-8wxz: Falcilysin in complex with hemoglobin beta chain peptide -

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Basic information

Entry
Database: PDB / ID: 8wxz
TitleFalcilysin in complex with hemoglobin beta chain peptide
Components
  • Falcilysin
  • Hemoglobin subunit beta 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 / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex ...hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / 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 / platelet aggregation / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / 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, beta-type ...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, beta-type / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER / Hemoglobin subunit beta / Falcilysin
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 beta fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,1495
Polymers136,9172
Non-polymers2323
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-43 kcal/mol
Surface area42150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.090, 105.870, 114.910
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 beta fragment


Mass: 1879.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 304 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.12M monosaccharides, 0.1M imidazole/MES monohydrate pH 6.5, 20% v/v PEG 500, 10% w/v PEG 20000

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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: 2.3→48.08 Å / Num. obs: 51607 / % possible obs: 99.91 % / Redundancy: 7.4 % / Biso Wilson estimate: 36.89 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1428 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 7.1 % / Num. unique obs: 5041 / CC1/2: 0.748 / CC star: 0.925 / % possible all: 99.9

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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: 2.3→48.08 Å / SU ML: 0.2779 / Cross valid method: FREE R-VALUE / σ(F): 0.98 / Phase error: 25.6835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2505 4905 4.99 %
Rwork0.2048 93426 -
obs0.2071 51597 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 12 301 9257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00569133
X-RAY DIFFRACTIONf_angle_d0.811412292
X-RAY DIFFRACTIONf_chiral_restr0.04851340
X-RAY DIFFRACTIONf_plane_restr0.00421569
X-RAY DIFFRACTIONf_dihedral_angle_d14.56783459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.31641610.2823043X-RAY DIFFRACTION99.2
2.33-2.350.31161670.27423146X-RAY DIFFRACTION99.88
2.35-2.380.32121630.263068X-RAY DIFFRACTION99.85
2.38-2.410.26991660.26513145X-RAY DIFFRACTION99.94
2.41-2.440.32671630.26313115X-RAY DIFFRACTION99.85
2.44-2.480.30921650.25493149X-RAY DIFFRACTION99.88
2.48-2.510.26011540.25383062X-RAY DIFFRACTION99.66
2.51-2.550.30581610.24993105X-RAY DIFFRACTION99.73
2.55-2.590.31841670.24023133X-RAY DIFFRACTION99.88
2.59-2.630.3141640.24083107X-RAY DIFFRACTION99.94
2.63-2.680.29531610.23543133X-RAY DIFFRACTION99.94
2.68-2.730.27521680.23583133X-RAY DIFFRACTION100
2.73-2.780.26821620.23153115X-RAY DIFFRACTION100
2.78-2.840.24491670.21383099X-RAY DIFFRACTION100
2.84-2.90.27921650.2153149X-RAY DIFFRACTION100
2.9-2.970.26251640.21713085X-RAY DIFFRACTION99.97
2.97-3.040.26251690.20293131X-RAY DIFFRACTION99.97
3.04-3.120.27421640.21523121X-RAY DIFFRACTION100
3.12-3.210.28211630.21133131X-RAY DIFFRACTION100
3.21-3.320.23381660.21053110X-RAY DIFFRACTION100
3.32-3.440.25851620.19963123X-RAY DIFFRACTION99.97
3.44-3.570.25841650.18143096X-RAY DIFFRACTION99.97
3.57-3.740.22961650.18363123X-RAY DIFFRACTION99.91
3.74-3.930.22881630.17783142X-RAY DIFFRACTION99.94
3.93-4.180.19891600.1753076X-RAY DIFFRACTION99.85
4.18-4.50.22161660.16423121X-RAY DIFFRACTION99.58
4.5-4.950.18941620.17123125X-RAY DIFFRACTION99.88
4.95-5.670.23711610.20123119X-RAY DIFFRACTION99.79
5.67-7.140.28671600.22283126X-RAY DIFFRACTION99.97
7.14-48.080.22621610.19373095X-RAY DIFFRACTION99.33

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