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- PDB-6o2x: Structure of cruzain bound to MMTS inhibitor -

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Basic information

Entry
Database: PDB / ID: 6o2x
TitleStructure of cruzain bound to MMTS inhibitor
ComponentsCruzipain
KeywordsHYDROLASE / Cysteine protease / Autocatalytic cleavage / Protease
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
PHOSPHATE ION / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.193 Å
AuthorsSilva, E.B. / Dall, E. / Ferreira, R.S. / Brandstetter, H.
Funding support Brazil, Austria, 5items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Austrian Science Fund Austria
LOreal-UNESCO
Minas Gerais State Agency for Research and Development
Coordination for the Improvement of Higher Education Personnel
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Cruzain structures: apocruzain and cruzain bound to S-methyl thiomethanesulfonate and implications for drug design.
Authors: Barbosa da Silva, E. / Dall, E. / Briza, P. / Brandstetter, H. / Ferreira, R.S.
History
DepositionFeb 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cruzipain
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9909
Polymers45,5222
Non-polymers4677
Water10,521584
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1046
Polymers22,7611
Non-polymers3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8853
Polymers22,7611
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.989, 72.369, 79.711
Angle α, β, γ (deg.)90.00, 91.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22761.227 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.26 M NaH2PO4, 0.14 M K2HPO4, with no other salts, no buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.19→53.57 Å / Num. obs: 115006 / % possible obs: 97 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.0509 / Net I/σ(I): 6.9
Reflection shellResolution: 1.19→1.21 Å / Rmerge(I) obs: 0.0592 / Num. unique obs: 23685

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKU

3kku


Resolution: 1.193→39.836 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1772 2003 1.75 %
Rwork0.1645 --
obs0.1647 114281 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.193→39.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 29 584 3803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0233354
X-RAY DIFFRACTIONf_angle_d1.0534589
X-RAY DIFFRACTIONf_dihedral_angle_d20.6131149
X-RAY DIFFRACTIONf_chiral_restr0.075504
X-RAY DIFFRACTIONf_plane_restr0.006594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.193-1.22280.2411410.24957813X-RAY DIFFRACTION94
1.2228-1.25590.23421430.23757844X-RAY DIFFRACTION95
1.2559-1.29280.25711380.22367898X-RAY DIFFRACTION95
1.2928-1.33460.19761340.20877801X-RAY DIFFRACTION94
1.3346-1.38230.22281480.197999X-RAY DIFFRACTION96
1.3823-1.43760.20431410.18767927X-RAY DIFFRACTION95
1.4376-1.50310.17881430.16887952X-RAY DIFFRACTION95
1.5031-1.58230.19821350.16137846X-RAY DIFFRACTION95
1.5823-1.68140.17891470.14528038X-RAY DIFFRACTION97
1.6814-1.81130.14261400.14538197X-RAY DIFFRACTION98
1.8113-1.99350.16641460.14218097X-RAY DIFFRACTION97
1.9935-2.2820.14011490.1368262X-RAY DIFFRACTION99
2.282-2.87490.181500.14828185X-RAY DIFFRACTION98
2.8749-39.85820.15561480.1588419X-RAY DIFFRACTION99

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