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- PDB-8ev4: NlpC B3 - Trichomonas Vaginalis -

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Basic information

Entry
Database: PDB / ID: 8ev4
TitleNlpC B3 - Trichomonas Vaginalis
ComponentsClan CA, family C40, NlpC/P60 superfamily cysteine peptidasePapain-like protease
KeywordsHYDROLASE / NlpC / P60 / CHAP / NlpC/P60 / Cysteine Protease
Function / homologyNlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily / Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase
Function and homology information
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBarnett, M.J. / Goldstone, D.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: Plos Pathog. / Year: 2023
Title: NlpC/P60 peptidoglycan hydrolases of Trichomonas vaginalis have complementary activities that empower the protozoan to control host-protective lactobacilli.
Authors: Barnett, M.J. / Pinheiro, J. / Keown, J.R. / Biboy, J. / Gray, J. / Lucinescu, I.W. / Vollmer, W. / Hirt, R.P. / Simoes-Barbosa, A. / Goldstone, D.C.
History
DepositionOct 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase


Theoretical massNumber of molelcules
Total (without water)13,2141
Polymers13,2141
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.050, 34.050, 181.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase / Papain-like protease


Mass: 13214.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_042760 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR / References: UniProt: A2FQ38
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.26 M Ammonium Sulfate, 0.1 M Tris pH 8.5. / Temp details: 18 degrees Celsius

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→33.47 Å / Num. obs: 27581 / % possible obs: 99.94 % / Redundancy: 2 % / Biso Wilson estimate: 12.09 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01919 / Rpim(I) all: 0.01919 / Rrim(I) all: 0.02714 / Net I/av σ(I): 14.66 / Net I/σ(I): 13.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3937 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2662 / CC1/2: 0.619 / CC star: 0.874 / Rpim(I) all: 0.3937 / Rrim(I) all: 0.5568 / % possible all: 99.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BIM

6bim


Resolution: 1.3→33.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.39 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16827 1386 5 %RANDOM
Rwork0.14713 ---
obs0.14823 26195 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.895 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.3→33.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 0 66 901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019895
X-RAY DIFFRACTIONr_bond_other_d0.0020.02832
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9461217
X-RAY DIFFRACTIONr_angle_other_deg0.92231924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6222.64734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.73615140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.195155
X-RAY DIFFRACTIONr_chiral_restr0.0840.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02215
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_it1.1861.231475
X-RAY DIFFRACTIONr_mcbond_other1.1821.23474
X-RAY DIFFRACTIONr_mcangle_it1.4971.857596
X-RAY DIFFRACTIONr_mcangle_other1.4971.857597
X-RAY DIFFRACTIONr_scbond_it1.3851.462420
X-RAY DIFFRACTIONr_scbond_other1.3841.462420
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7952.112613
X-RAY DIFFRACTIONr_long_range_B_refined2.58510.8611000
X-RAY DIFFRACTIONr_long_range_B_other2.36510.6982
X-RAY DIFFRACTIONr_rigid_bond_restr1.1631727
X-RAY DIFFRACTIONr_sphericity_free21.553523
X-RAY DIFFRACTIONr_sphericity_bonded7.59251743
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 102 -
Rwork0.271 1855 -
obs--99.29 %

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