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- PDB-6ux6: Cruzain covalently bound by a vinylsulfone compound -

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Basic information

Entry
Database: PDB / ID: 6ux6
TitleCruzain covalently bound by a vinylsulfone compound
ComponentsCruzipain
KeywordsHYDROLASE / Cruzain / vinylSulfone / covalent / inhibitor
Function / homology
Function and homology information


cruzipain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-TM8 / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsZhai, X. / Tang, S. / Chenna, B.C. / Meek, T.D. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH) United States
CitationJournal: To Be Published
Title: Cruzain covalently bound by a vinylsulfone compound
Authors: Zhai, X. / Tang, S. / Chenna, B.C. / Meek, T.D. / Sacchettini, J.C.
History
DepositionNov 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3783
Polymers22,7151
Non-polymers6632
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.509, 122.127, 34.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P25779, cruzipain
#2: Chemical ChemComp-TM8 / Nalpha-[(benzyloxy)carbonyl]-N-[(2S)-1-phenyl-4-(phenylsulfonyl)butan-2-yl]-L-phenylalaninamide


Mass: 570.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 1.88 Å3/Da / Density % sol: 34.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 13196 / % possible obs: 98.2 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.056 / Rrim(I) all: 0.137 / Χ2: 2.656 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.975.20.2415770.9310.1180.2691.30288.5
1.97-2.015.50.2366170.9210.1130.2631.53793.5
2.01-2.056.20.2326540.9340.1020.2541.59398.5
2.05-2.096.40.2356250.9430.1040.2581.93599.4
2.09-2.146.20.2046690.9690.090.2241.90599
2.14-2.186.10.2046470.9690.0910.2242.07198.6
2.18-2.2460.2016490.9480.0910.2222.37499.5
2.24-2.35.90.1886550.9550.0860.2082.38498.3
2.3-2.3760.1836430.9710.0820.2022.61298.3
2.37-2.445.90.1746600.9680.0770.1912.60299.7
2.44-2.535.90.1666640.970.0750.1832.63198.8
2.53-2.635.80.1536430.9710.0690.1682.74399.4
2.63-2.755.80.1566760.9750.0720.1723.18199.4
2.75-2.95.60.1476700.9620.0690.1633.14298.8
2.9-3.085.90.1366520.980.0630.153.3399.1
3.08-3.325.80.1246770.9770.0570.1373.38799.4
3.32-3.655.70.1256710.9730.0570.1383.65198.5
3.65-4.185.80.1216820.9850.0540.1333.81298.7
4.18-5.2660.1016960.9870.0450.1113.57999
5.26-506.10.0957690.9860.0410.1032.9299

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ME4

1me4


Resolution: 1.94→33.756 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 29.18
RfactorNum. reflection% reflection
Rfree0.2685 645 4.9 %
Rwork0.2212 --
obs0.2235 13156 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.19 Å2 / Biso mean: 28.6582 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 1.94→33.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 47 70 1706
Biso mean--29.31 29.15 -
Num. residues----215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.94-2.08660.37261220.2741232994
2.0866-2.29660.31221170.2706250399
2.2966-2.62880.30221300.2604247899
2.6288-3.31150.33971450.2403252699
3.3115-33.750.18511310.1767267599
Refinement TLS params.Method: refined / Origin x: 2.9971 Å / Origin y: -15.3025 Å / Origin z: -12.9272 Å
111213212223313233
T0.1775 Å20.0312 Å20.0164 Å2-0.1831 Å20.0011 Å2--0.1725 Å2
L0.1593 °20.2159 °20.0119 °2-0.2264 °2-0.0255 °2--0.1441 °2
S-0.0315 Å °-0.0195 Å °-0.0328 Å °-0.0087 Å °0.0125 Å °0.0124 Å °0.0138 Å °-0.0016 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 215
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allE1 - 70

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