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- PDB-2aim: CRUZAIN INHIBITED WITH BENZOYL-ARGININE-ALANINE-FLUOROMETHYLKETONE -

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Basic information

Entry
Database: PDB / ID: 2aim
TitleCRUZAIN INHIBITED WITH BENZOYL-ARGININE-ALANINE-FLUOROMETHYLKETONE
ComponentsCRUZAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEASE / TRYPANOSOMA CRUZI / PROTEINASE / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 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
BENZOYL-ARGININE-ALANINE-FLUORO-METHYL KETONE / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGillmor, S.A. / Fletterick, R.J.
Citation
Journal: Protein Sci. / Year: 1997
Title: Structural determinants of specificity in the cysteine protease cruzain.
Authors: Gillmor, S.A. / Craik, C.S. / Fletterick, R.J.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Production of Crystallizable Cruzain, the Major Cysteine Protease from Trypanosoma Cruzi
Authors: Eakin, A.E. / Mcgrath, M.E. / Mckerrow, J.H. / Fletterick, R.J. / Craik, C.S.
History
DepositionApr 21, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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 1.4Oct 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: CRUZAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1132
Polymers22,7151
Non-polymers3971
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.160, 51.600, 45.200
Angle α, β, γ (deg.)90.00, 115.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRUZAIN / CRUZIPAIN


Mass: 22715.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: GLY 213 STOP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: TULAHUEN / Cellular location: LYSOSOME, SURFACE / Organelle: LYSOSOME / Plasmid: PLOXCHEYCDELTAC / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA
References: UniProt: P25779, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-ZRA / BENZOYL-ARGININE-ALANINE-FLUORO-METHYL KETONE / benzyl [(2S)-5-[(diaminomethyl)amino]-1-{[(2S)-4-fluoro-3-oxobutan-2-yl]amino}-1-oxopentan-2-yl]carbamate


Type: peptide-like / Mass: 397.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28FN5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 33 %
Crystal growMethod: vapor diffusion -hanging drop -microseeding / pH: 5
Details: 0.9 M NACITRATE, PH 5.0. CRYSTALS WERE PRODUCED BY MICROSEEDING HANGING DROPS, vapor diffusion -hanging drop -microseeding
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.7-1.0 Msodium citrate1reservoir
213-18 mg/mlcruzain1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 1, 1994
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 8106 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.35 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 2 / Rsym value: 0.178 / % possible all: 82
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameVersionClassification
UCSDSOFTWAREdata collection
UCSDSOFTWAREdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
UCSDdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRUZAIN

Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 595 7.5 %RANDOM
Rwork0.186 ---
obs0.186 7935 90 %-
Displacement parametersBiso mean: 8.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 27 52 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it1.51.5
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it22
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 71 6.3 %
Rwork0.207 7935 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19SG.PROTOPH19SG.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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