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- PDB-3i06: Crystal structure of cruzain covalently bound to a purine nitrile -

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Basic information

Entry
Database: PDB / ID: 3i06
TitleCrystal structure of cruzain covalently bound to a purine nitrile
ComponentsCruzipain
KeywordsHYDROLASE / Autocatalytic cleavage / Glycoprotein / Protease / Thiol protease / Zymogen
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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-QL2 / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsFerreira, R.S. / Shoichet, B.K. / McKerrow, J.H.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Identification and optimization of inhibitors of trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB.
Authors: Mott, B.T. / Ferreira, R.S. / Simeonov, A. / Jadhav, A. / Ang, K.K. / Leister, W. / Shen, M. / Silveira, J.T. / Doyle, P.S. / Arkin, M.R. / McKerrow, J.H. / Inglese, J. / Austin, C.P. / ...Authors: Mott, B.T. / Ferreira, R.S. / Simeonov, A. / Jadhav, A. / Ang, K.K. / Leister, W. / Shen, M. / Silveira, J.T. / Doyle, P.S. / Arkin, M.R. / McKerrow, J.H. / Inglese, J. / Austin, C.P. / Thomas, C.J. / Shoichet, B.K. / Maloney, D.J.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)23,0152
Polymers22,7151
Non-polymers3001
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.967, 82.967, 101.895
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-438-

HOH

31A-458-

HOH

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 1 / Fragment: resudues 123-337
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-QL2 / 6-[(3,5-difluorophenyl)amino]-9-ethyl-9H-purine-2-carbonitrile


Mass: 300.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10F2N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 2.0 M NH4H2PO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→41.48 Å / Num. obs: 77795 / % possible obs: 92.7 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 8.399
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.1-1.164.30.4071.93382377810.40765.1
1.16-1.237.40.292.67142996830.2985.5
1.23-1.31120.2423.1128197106800.24299
1.31-1.4213.70.1664.513724799890.16699.6
1.42-1.5613.70.1027.112742692700.10299.9
1.56-1.7413.70.06710.611584484560.067100
1.74-2.0113.60.04613.710212675070.046100
2.01-2.4613.40.04812.48549864000.048100
2.46-3.4812.70.03217.56456250680.032100
3.48-41.5613.20.02616.63921929610.02699.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.51 Å
Translation2.5 Å41.51 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ME3

1me3


Resolution: 1.1→41.48 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.138 / WRfactor Rwork: 0.119 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.938 / SU B: 0.711 / SU ML: 0.016 / SU R Cruickshank DPI: 0.026 / SU Rfree: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.142 3940 5.1 %RANDOM
Rwork0.119 ---
obs0.12 77748 92.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.33 Å2 / Biso mean: 10.649 Å2 / Biso min: 2.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.1→41.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 23 338 2057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211787
X-RAY DIFFRACTIONr_bond_other_d0.0050.021126
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.9412480
X-RAY DIFFRACTIONr_angle_other_deg1.5463.0042787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6385250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31126.10477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63215261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.418153
X-RAY DIFFRACTIONr_chiral_restr0.1170.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022089
X-RAY DIFFRACTIONr_gen_planes_other0.010.02341
X-RAY DIFFRACTIONr_nbd_refined0.3060.2372
X-RAY DIFFRACTIONr_nbd_other0.2040.21268
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2892
X-RAY DIFFRACTIONr_nbtor_other0.0940.2862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3830.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.234
X-RAY DIFFRACTIONr_mcbond_it2.1181.51437
X-RAY DIFFRACTIONr_mcbond_other0.8711.5468
X-RAY DIFFRACTIONr_mcangle_it2.6121826
X-RAY DIFFRACTIONr_scbond_it3.6553811
X-RAY DIFFRACTIONr_scangle_it4.3034.5633
X-RAY DIFFRACTIONr_rigid_bond_restr1.80433733
X-RAY DIFFRACTIONr_sphericity_free12.43344
X-RAY DIFFRACTIONr_sphericity_bonded4.84332845
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 185 -
Rwork0.258 3476 -
all-3661 -
obs--60 %

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