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- PDB-8ev5: NlpC B3 covalently bound with E64 inhibitor fragment -

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Basic information

Entry
Database: PDB / ID: 8ev5
TitleNlpC B3 covalently bound with E64 inhibitor fragment
ComponentsClan CA, family C40, NlpC/P60 superfamily cysteine peptidase
KeywordsHYDROLASE/Inhibitor / NlpC / P60 / CHAP / NlpC/P60 / Cysteine Protease / inhibitor / E64 / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homology: / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / Chem-E64 / Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6713
Polymers13,2141
Non-polymers4562
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.020, 34.020, 180.878
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


Mass: 13214.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_042760 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR / References: UniProt: A2FQ38
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.89 %
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: 1.65→33.43 Å / Num. obs: 13697 / % possible obs: 99.55 % / Redundancy: 2 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01579 / Rpim(I) all: 0.01579 / Rrim(I) all: 0.02232 / Net I/av σ(I): 15.48 / Net I/σ(I): 14.3
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2959 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2561 / CC1/2: 0.755 / CC star: 0.928 / Rpim(I) all: 0.2959 / Rrim(I) all: 0.4184 / % possible all: 95.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→33.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.815 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18887 716 5.2 %RANDOM
Rwork0.17095 ---
obs0.17191 12981 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.65→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 14 64 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019897
X-RAY DIFFRACTIONr_bond_other_d0.0020.02795
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9581216
X-RAY DIFFRACTIONr_angle_other_deg0.9293.0011850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45322.64734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82815135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.789155
X-RAY DIFFRACTIONr_chiral_restr0.0740.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
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_it1.0521.738471
X-RAY DIFFRACTIONr_mcbond_other1.051.737470
X-RAY DIFFRACTIONr_mcangle_it1.6912.602590
X-RAY DIFFRACTIONr_mcangle_other1.6912.603591
X-RAY DIFFRACTIONr_scbond_it1.4221.965426
X-RAY DIFFRACTIONr_scbond_other1.3981.929420
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0632.835614
X-RAY DIFFRACTIONr_long_range_B_refined3.52220.732971
X-RAY DIFFRACTIONr_long_range_B_other3.5220.69970
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 48 -
Rwork0.311 912 -
obs--96.29 %

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