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- PDB-6n3s: Crystal structure of apo-cruzain -

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Basic information

Entry
Database: PDB / ID: 6n3s
TitleCrystal structure of apo-cruzain
ComponentsCruzipain
KeywordsHYDROLASE / apo cruzain / protease / thiol 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 ...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. / Rodrigues, F.T.G. / Ferreira, R.S. / Brandstetter, H.
Funding support Brazil, Austria, 4items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Austrian Science Fund Austria
Other privateCAPES Brazil
Other privateL'Oreal-UNESCO Brazil
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
DepositionNov 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cruzipain
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9319
Polymers45,4302
Non-polymers5007
Water9,260514
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0916
Polymers22,7151
Non-polymers3765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8393
Polymers22,7151
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.830, 72.210, 79.820
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 2 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express / References: UniProt: P25779, cruzipain
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.26 M NaH2PO4.H2O 0.14 M K2HPO4 / PH range: 5.6-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.19→36.11 Å / Num. obs: 115537 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 8.67 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.046 / Rrim(I) all: 0.088 / Net I/σ(I): 8.6
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5760 / CC1/2: 0.64 / Rpim(I) all: 0.29 / Rrim(I) all: 0.56 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLM7.2.0data reduction
Aimless1.10.26data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KKU

3kku


Resolution: 1.193→34.92 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1652 6001 5.2 %
Rwork0.1379 --
obs0.1393 115506 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.193→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 30 514 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083357
X-RAY DIFFRACTIONf_angle_d0.9914596
X-RAY DIFFRACTIONf_dihedral_angle_d21.4721149
X-RAY DIFFRACTIONf_chiral_restr0.08501
X-RAY DIFFRACTIONf_plane_restr0.006599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.193-1.20650.30982140.26973651X-RAY DIFFRACTION98
1.2065-1.22070.3022010.25833688X-RAY DIFFRACTION98
1.2207-1.23560.27392240.24353562X-RAY DIFFRACTION98
1.2356-1.25130.25721960.23883606X-RAY DIFFRACTION97
1.2513-1.26770.23622010.23043647X-RAY DIFFRACTION97
1.2677-1.28510.28391940.22273578X-RAY DIFFRACTION97
1.2851-1.30350.24192060.22253577X-RAY DIFFRACTION96
1.3035-1.32290.24672110.20073590X-RAY DIFFRACTION97
1.3229-1.34360.21722100.18623623X-RAY DIFFRACTION98
1.3436-1.36560.20452090.17753686X-RAY DIFFRACTION98
1.3656-1.38920.20012150.16843577X-RAY DIFFRACTION97
1.3892-1.41440.20832090.16913667X-RAY DIFFRACTION98
1.4144-1.44160.18712200.1633577X-RAY DIFFRACTION97
1.4416-1.47110.17811820.15153657X-RAY DIFFRACTION97
1.4711-1.50310.15631830.13183607X-RAY DIFFRACTION96
1.5031-1.5380.1641690.12213568X-RAY DIFFRACTION96
1.538-1.57650.16521930.11763701X-RAY DIFFRACTION98
1.5765-1.61910.14381940.1113669X-RAY DIFFRACTION98
1.6191-1.66670.12912080.10483646X-RAY DIFFRACTION98
1.6667-1.72050.13762260.10153679X-RAY DIFFRACTION98
1.7205-1.7820.15591800.10583627X-RAY DIFFRACTION98
1.782-1.85340.13612080.10663638X-RAY DIFFRACTION97
1.8534-1.93770.12672070.1043651X-RAY DIFFRACTION98
1.9377-2.03990.13811870.10253733X-RAY DIFFRACTION99
2.0399-2.16770.12392220.10453656X-RAY DIFFRACTION99
2.1677-2.3350.12961880.10463705X-RAY DIFFRACTION98
2.335-2.56990.13181980.11723631X-RAY DIFFRACTION97
2.5699-2.94160.15491560.12553739X-RAY DIFFRACTION98
2.9416-3.70550.13951940.13223764X-RAY DIFFRACTION100
3.7055-34.93530.16971960.14593805X-RAY DIFFRACTION99

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