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- PDB-7s18: Crystal structure of cruzain with gallinamide analog from 2-biary... -

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Basic information

Entry
Database: PDB / ID: 7s18
TitleCrystal structure of cruzain with gallinamide analog from 2-biaryl series
ComponentsCruzipain
KeywordsHYDROLASE / Cysteine Protease / Cruzain / Gallinamide
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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / Chem-83E / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSharma, V. / Podust, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI127505 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi .
Authors: Barbosa Da Silva, E. / Sharma, V. / Hernandez-Alvarez, L. / Tang, A.H. / Stoye, A. / O'Donoghue, A.J. / Gerwick, W.H. / Payne, R.J. / McKerrow, J.H. / Podust, L.M.
History
DepositionSep 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)23,5372
Polymers22,7151
Non-polymers8221
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.500, 99.500, 85.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 1
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-83E / N,N-dimethyl-L-valyl-L-leucyl-N-[(3S)-6-{(2S)-2-[([1,1'-biphenyl]-4-yl)methyl]-3-methoxy-5-oxo-2,5-dihydro-1H-pyrrol-1-yl}-6-oxo-1-phenylhexan-3-yl]-L-leucinamide


Mass: 822.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H67N5O6 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002486
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.11 % / Description: transparent rhomboid shaped crystals
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 3.2 M Sodium Chloride; 0.1 M Sodium Citrate pH 5.3; 0.01 M Sarcosine

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2021 / Details: Mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.14→70.36 Å / Num. obs: 12135 / % possible obs: 100 % / Redundancy: 25.246 % / Biso Wilson estimate: 79.502 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.07 / Χ2: 0.828 / Net I/σ(I): 21.31 / Num. measured all: 306358 / Scaling rejects: 163
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.14-2.226.7495.5730.898710.4815.68100
2.2-2.2626.4193.8451.398630.7423.91999.9
2.26-2.3225.2112.5232.288240.8862.57599.9
2.32-2.3925.3072.1292.738170.9212.17299.9
2.39-2.4727.2621.7423.587930.9581.775100
2.47-2.5626.9011.34.757610.9681.32599.9
2.56-2.6526.5560.9336.37370.9820.95199.7
2.65-2.7625.7260.5299.47120.9930.54100
2.76-2.8924.6960.33213.226770.9970.339100
2.89-3.0326.5260.23218.426600.9980.237100
3.03-3.1926.390.15125.46280.9990.155100
3.19-3.3826.0290.10433.285890.9990.107100
3.38-3.6223.8560.07342.815640.9990.075100
3.62-3.9123.2390.05851.735280.9990.059100
3.91-4.2824.3960.04857.644820.9990.049100
4.28-4.7923.1660.04760.1144510.048100
4.79-5.5321.3450.04859.883970.9990.0599.7
5.53-6.7722.4570.04562.013410.9990.046100
6.77-9.5720.7830.04262.72720.9990.043100
9.57-70.3617.9430.03758.3617410.038100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kku

3kku


Resolution: 2.14→70.36 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.231 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2894 568 4.7 %RANDOM
Rwork0.1971 ---
obs0.2013 11556 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.07 Å2 / Biso mean: 87.414 Å2 / Biso min: 47.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å2-0 Å20 Å2
2--3.73 Å2-0 Å2
3----7.46 Å2
Refinement stepCycle: final / Resolution: 2.14→70.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 60 3 1652
Biso mean--94.27 75.2 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191695
X-RAY DIFFRACTIONr_bond_other_d0.0020.021517
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9542323
X-RAY DIFFRACTIONr_angle_other_deg1.0233487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.935214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74825.67267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61115230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.719153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02389
LS refinement shellResolution: 2.14→2.196 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 28 -
Rwork0.495 842 -
all-870 -
obs--100 %

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