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- PDB-9h6r: X-ray structure of Hydrogenosomal processing peptidase (HPP), E56... -

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Basic information

Entry
Database: PDB / ID: 9h6r
TitleX-ray structure of Hydrogenosomal processing peptidase (HPP), E56Q inactive mutant, from Trichomonas vaginalis co-crystallized with presequence peptide from ferredoxin oxidoreductase (PFO) - not visible in the structure model
Components
  • Alpha-MPP
  • Clan ME, family M16, insulinase-like metallopeptidase
KeywordsHYDROLASE / hydrogenosomal processing peptidase / Zinc metallopeptidase / ortholog of mitochondrial processing peptidase
Function / homology
Function and homology information


metallopeptidase activity / mitochondrion / metal ion binding
Similarity search - Function
: / 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
Clan ME, family M16, insulinase-like metallopeptidase / Clan ME, family M16, insulinase-like metallopeptidase
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSamad, A. / Barinka, C. / Motlova, L. / Cianci, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray structure of Hydrogenosomal processing peptidase (HPP), E56Q inactive mutant, from Trichomonas vaginalis co-crystallized with presequence peptide from ferredoxin oxidoreductase (PFO) - ...Title: X-ray structure of Hydrogenosomal processing peptidase (HPP), E56Q inactive mutant, from Trichomonas vaginalis co-crystallized with presequence peptide from ferredoxin oxidoreductase (PFO) - not visible in the structure model
Authors: Samad, A. / Barinka, C. / Motlova, L. / Cianci, M.
History
DepositionOct 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-MPP
B: Clan ME, family M16, insulinase-like metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,18711
Polymers94,3572
Non-polymers8309
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-141 kcal/mol
Surface area35070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.241, 115.026, 124.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha-MPP / alpha subunit of hydrogenosomal processing peptidase (HPP)


Mass: 47480.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_119710 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2D7B7
#2: Protein Clan ME, family M16, insulinase-like metallopeptidase / beta subunit of hydrogenosomal processing peptidase (HPP)


Mass: 46876.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: There is a substrate missing in this model PFO, residues 1-7, MLRNFSK. The map is there but not clear enough to fit the peptide.
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_233350 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2ES04

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Non-polymers , 4 types, 137 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.33 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate [pH 6.0], 2.0 M ammonium sulfate and 0.2 mM n-dodecylmaltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.65→115.03 Å / Num. obs: 37405 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.991 / Rpim(I) all: 0.109 / Net I/σ(I): 9
Reflection shellResolution: 2.65→2.77 Å / Redundancy: 14 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4500 / CC1/2: 0.493 / Rpim(I) all: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.135 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23995 1830 4.9 %RANDOM
Rwork0.18568 ---
obs0.18837 35513 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.25 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.65→84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 42 128 6498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9678811
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.35925.16281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.755151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0441523
X-RAY DIFFRACTIONr_chiral_restr0.1270.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214823
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8355.2033241
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.9047.7894047
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4945.6113260
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.71242.9079725
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 123 -
Rwork0.264 2580 -
obs--100 %

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