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- PDB-1me4: High Resolution Crystal Structure Analysis Of Cruzain non-covalen... -

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Basic information

Entry
Database: PDB / ID: 1me4
TitleHigh Resolution Crystal Structure Analysis Of Cruzain non-covalently Bound To A Hydroxymethyl Ketone Inhibitor (I)
ComponentsCRUZIPAIN
KeywordsHYDROLASE / cysteine protease / non-covalent inhibitor
Function / homology
Function and homology information


cruzipain / cysteine-type endopeptidase activity / proteolysis
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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-T10 / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBrinen, L.S. / Huang, L. / Ellman, J.A.
Citation
Journal: Bioorg.Med.Chem. / Year: 2003
Title: Crystal Structures of Reversible Ketone-based Inhibitors of the Cysteine Protease Cruzain
Authors: Huang, L. / Brinen, L.S. / Ellman, J.A.
#1: Journal: Structure / Year: 2000
Title: A target within the target: probing cruzain's P1' site to define structural determinants for the Chagas' disease protease.
Authors: Brinen, L.S. / Hansell, E. / Cheng, J. / Roush, W.R. / McKerrow, J.H. / Fletterick, R.J.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: THE CRYSTAL STRUCTURE OF CRUZAIN: A THERAPEUTIC TARGET FOR CHAGAS' DISEASE
Authors: MCGRATH, M.E. / EAKIN, A.E. / ENGEL, J.C. / MCKERROW, J.H. / CRAIK, C.S. / FLETTERICK, R.J.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)23,1762
Polymers22,7151
Non-polymers4611
Water8,719484
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.523, 51.712, 46.040
Angle α, β, γ (deg.)90.00, 116.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer

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Components

#1: Protein CRUZIPAIN / Major cysteine proteinase / Cruzaine / Cruzain


Mass: 22715.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: DH5ALPHA / Production host: Escherichia coli (E. coli)
References: UniProt: P25779, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-T10 / [1-(1-BENZYL-3-HYDROXY-2-OXO-PROPYLCARBAMOYL)-2-PHENYL-ETHYL]-CARBAMIC ACID BENZYL ESTER


Mass: 460.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.6 - 1.0 M Sodium Citrate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.6-1.0 Msodium citrate1reservoirpH6.6-7.0
22 mMBis-Tris1droppH5.8
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 51125 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 26.7
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 6.02 / Num. unique all: 3370 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 53954 / Num. measured all: 440603
Reflection shell
*PLUS
% possible obs: 91.1 %

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1f29

1f29


Resolution: 1.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Num. reflectionSelection details
all52264 -
obs47929 -
Rfree-Random
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 34 484 2111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.068
X-RAY DIFFRACTIONs_approx_iso_adps0.083
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_from_restr_planes0.0297
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection Rfree: 1631 / % reflection Rfree: 10 % / Rfactor all: 0.096 / Rfactor Rfree: 0.13 / Rfactor Rwork: 0.0969
Solvent computation
*PLUS
Displacement parameters
*PLUS

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