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- PDB-1me3: High Resolution Crystal Structure Analysis Of Cruzain non-covalen... -

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Basic information

Entry
Database: PDB / ID: 1me3
TitleHigh Resolution Crystal Structure Analysis Of Cruzain non-covalently Bound To A Hydroxymethyl Ketone Inhibitor (II)
ComponentsCruzipain
KeywordsHYDROLASE / cysteine protease / non-covalent inhibitor
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-P10 / 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: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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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)23,1912
Polymers22,7151
Non-polymers4761
Water9,872548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.570, 51.590, 45.950
Angle α, β, γ (deg.)90.00, 116.62, 90.00
Int Tables number4
Space group name H-MP1211

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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-P10 / [1-(3-HYDROXY-2-OXO-1-PHENETHYL-PROPYLCARBAMOYL)2-PHENYL-ETHYL]-CARBAMIC ACID PYRIDIN-4-YLMETHYL ESTER


Mass: 475.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29N3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 291 K / pH: 6.8
Details: 0.6 - 1.0 M Sodium Citrate, pH 6.8, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop
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, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 42575 / Num. obs: 42575 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 25
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 11.8 / Num. unique all: 3912 / % possible all: 97.8
Reflection
*PLUS
Num. obs: 43377 / Num. measured all: 252261 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F2A

1f2a


Resolution: 1.2→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1346 4792 Random
Rwork0.093 --
all0.1048 42575 -
obs0.1033 42575 -
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 35 551 2202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_from_restr_planes0.0312
X-RAY DIFFRACTIONs_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_similar_dist0.034
X-RAY DIFFRACTIONs_approx_iso_adps0.079
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.135 / Rfactor Rwork: 0.0939
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.029

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