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- PDB-9h5r: X-ray structure of Trichomonas vaginalis inactive mutant hydrogen... -

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Basic information

Entry
Database: PDB / ID: 9h5r
TitleX-ray structure of Trichomonas vaginalis inactive mutant hydrogenosomal processing peptidase heterodimer (HPPin)
Components
  • Alpha-MPP
  • Clan ME, family M16, insulinase-like metallopeptidase
KeywordsHYDROLASE / hydrogenosomal processing peptidase / Zinc metalloprotease / Trichomonas vaginalis
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: 2.84 Å
AuthorsSamad, A. / Cianci, M. / Motlova, L. / Barinka, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray structure of Trichomonas vaginalis inactive mutant hydrogenosomal processing peptidase heterodimer (HPPin)
Authors: Samad, A. / Cianci, M. / Motlova, L. / Barinka, C.
History
DepositionOct 23, 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)94,9999
Polymers94,3572
Non-polymers6427
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-129 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.910, 115.100, 125.115
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 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
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_233350 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2ES04
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
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: 3.35 Å3/Da / Density % sol: 63.33 %
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 0.2 mM n-dodecylmaltoside

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.84→125.11 Å / Num. obs: 30574 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.067 / Rrim(I) all: 0.147 / Net I/σ(I): 12 / Num. measured all: 138677
Reflection shellResolution: 2.84→2.99 Å / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.905 / Num. measured all: 20135 / Num. unique obs: 4370 / CC1/2: 0.649 / Rpim(I) all: 0.467 / Rrim(I) all: 1.021 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.7data scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→48 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.878 / SU B: 15.378 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.832 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27324 1456 4.8 %RANDOM
Rwork0.20301 ---
obs0.20635 29064 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2---0.19 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.84→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6355 0 31 67 6453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196515
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9668827
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5075810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.12525.142282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.181151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1621523
X-RAY DIFFRACTIONr_chiral_restr0.1070.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214834
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_it3.135.7113249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.9978.5554056
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5735.9333266
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.90647.2059683
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: 2.84→2.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 115 -
Rwork0.314 2072 -
obs--99.91 %

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