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- PDB-7e3g: Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mu... -

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Basic information

Entry
Database: PDB / ID: 7e3g
TitleCrystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant in the living cell
ComponentsCysteine peptidase C (CPC)
KeywordsHYDROLASE / In cell crystal
Function / homology
Function and homology information


post-transcriptional regulation of gene expression / proteolysis involved in protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
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
Cysteine peptidase C (CPC)
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.86 Å
AuthorsAbe, S. / Pham, T.T. / Negishi, H. / Yamashita, K. / Hirata, K. / Ueno, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H05421 Japan
Japan Society for the Promotion of Science (JSPS)JP18K05140 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament.
Authors: Abe, S. / Pham, T.T. / Negishi, H. / Yamashita, K. / Hirata, K. / Ueno, T.
History
DepositionFeb 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine peptidase C (CPC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2193
Polymers37,2081
Non-polymers1,0112
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint15 kcal/mol
Surface area13410 Å2
Unit cell
Length a, b, c (Å)124.080, 124.080, 52.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Cysteine peptidase C (CPC)


Mass: 37207.676 Da / Num. of mol.: 1 / Mutation: R91C, T223C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.6.560 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: D6XHE1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 298 K / Method: in cell

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.86→50 Å / Num. obs: 4069 / % possible obs: 96.3 % / Redundancy: 5.4 % / CC1/2: 0.918 / Net I/σ(I): 3.48
Reflection shellResolution: 3.86→4.09 Å / Num. unique obs: 649 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PHENIXphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hwy

4hwy


Resolution: 3.86→48.756 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.899 / SU B: 38.422 / SU ML: 0.515 / Cross valid method: FREE R-VALUE / ESU R Free: 0.675
RfactorNum. reflection% reflection
Rfree0.2138 203 4.991 %
Rwork0.1766 3864 -
all0.178 --
obs-4067 96.764 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 74.122 Å2
Baniso -1Baniso -2Baniso -3
1--1.029 Å20 Å20 Å2
2---1.029 Å20 Å2
3---2.058 Å2
Refinement stepCycle: LAST / Resolution: 3.86→48.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 67 3 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132527
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172143
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.683451
X-RAY DIFFRACTIONr_angle_other_deg1.2041.6134996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.85306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46422.105133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.77215349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3971515
X-RAY DIFFRACTIONr_chiral_restr0.0560.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022872
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02567
X-RAY DIFFRACTIONr_nbd_refined0.2320.2631
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.22329
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21185
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.277
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.210
X-RAY DIFFRACTIONr_nbd_other0.170.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.23
X-RAY DIFFRACTIONr_mcbond_it4.9437.7151230
X-RAY DIFFRACTIONr_mcbond_other4.9327.7141229
X-RAY DIFFRACTIONr_mcangle_it8.02711.5561534
X-RAY DIFFRACTIONr_mcangle_other8.02711.5581535
X-RAY DIFFRACTIONr_scbond_it4.8788.2811297
X-RAY DIFFRACTIONr_scbond_other4.8728.2821297
X-RAY DIFFRACTIONr_scangle_it8.06612.2481917
X-RAY DIFFRACTIONr_scangle_other8.06512.251918
X-RAY DIFFRACTIONr_lrange_it11.57891.4472892
X-RAY DIFFRACTIONr_lrange_other11.57691.4452892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.86-3.960.197170.274276X-RAY DIFFRACTION98.3221
3.96-4.0690.251190.239273X-RAY DIFFRACTION98.983
4.069-4.1860.3130.226262X-RAY DIFFRACTION98.2143
4.186-4.3150.302140.211254X-RAY DIFFRACTION98.5294
4.315-4.4560.26110.162263X-RAY DIFFRACTION97.8571
4.456-4.6120.205150.162234X-RAY DIFFRACTION97.6471
4.612-4.7860.14890.151246X-RAY DIFFRACTION97.3282
4.786-4.980.185100.147223X-RAY DIFFRACTION97.0833
4.98-5.2010.164150.141216X-RAY DIFFRACTION97.8814
5.201-5.4540.17170.176202X-RAY DIFFRACTION98.2063
5.454-5.7480.19460.156199X-RAY DIFFRACTION96.6981
5.748-6.0950.27110.14194X-RAY DIFFRACTION98.0861
6.095-6.5130.191100.158181X-RAY DIFFRACTION96.9543
6.513-7.0320.21790.157164X-RAY DIFFRACTION95.5801
7.032-7.6980.11380.139163X-RAY DIFFRACTION97.7143
7.698-8.5980.1430.106142X-RAY DIFFRACTION95.3947
8.598-9.9130.18160.117126X-RAY DIFFRACTION93.617
9.913-12.1020.30430.147112X-RAY DIFFRACTION92.7419
12.102-16.9540.23360.27485X-RAY DIFFRACTION87.5
16.954-48.7560.25910.40449X-RAY DIFFRACTION74.6269

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