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- PDB-7e3e: Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant -

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Basic information

Entry
Database: PDB / ID: 7e3e
TitleCrystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant
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: 2.3 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
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint15 kcal/mol
Surface area13990 Å2
Unit cell
Length a, b, c (Å)125.100, 125.100, 55.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

21A-466-

HOH

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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.: 68 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 293 K / Method: in cell / Details: In cell crystallization

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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: Dec 5, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20010 / % possible obs: 100 % / Redundancy: 558 % / CC1/2: 0.99 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.32 Å / Num. unique obs: 496 / CC1/2: 0.374

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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: 2.3→46.764 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.498 / SU ML: 0.189 / Cross valid method: FREE R-VALUE / ESU R: 0.275 / ESU R Free: 0.233
RfactorNum. reflection% reflection
Rfree0.2728 1006 5.041 %
Rwork0.2213 18950 -
all0.224 --
obs-19956 99.9 %
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: 32.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.755 Å20 Å20 Å2
2--0.755 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 67 68 2514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132530
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172141
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.683453
X-RAY DIFFRACTIONr_angle_other_deg1.2331.6134994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18722.105133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3515351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0871515
X-RAY DIFFRACTIONr_chiral_restr0.0710.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
X-RAY DIFFRACTIONr_nbd_refined0.1840.2394
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.21896
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21184
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.26
X-RAY DIFFRACTIONr_nbd_other0.2380.220
X-RAY DIFFRACTIONr_symmetry_nbtor_refined0.250.21
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.22
X-RAY DIFFRACTIONr_mcbond_it2.2473.3151230
X-RAY DIFFRACTIONr_mcbond_other2.2393.3121229
X-RAY DIFFRACTIONr_mcangle_it3.5284.9531534
X-RAY DIFFRACTIONr_mcangle_other3.5274.9561535
X-RAY DIFFRACTIONr_scbond_it2.8583.7221299
X-RAY DIFFRACTIONr_scbond_other2.8563.7221299
X-RAY DIFFRACTIONr_scangle_it4.5715.4621919
X-RAY DIFFRACTIONr_scangle_other4.575.4641920
X-RAY DIFFRACTIONr_lrange_it5.837.6862636
X-RAY DIFFRACTIONr_lrange_other5.79437.692633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.457690.3821374X-RAY DIFFRACTION100
2.36-2.4240.385710.3411337X-RAY DIFFRACTION100
2.424-2.4950.332570.3141325X-RAY DIFFRACTION100
2.495-2.5710.293640.2961254X-RAY DIFFRACTION100
2.571-2.6560.319770.2621223X-RAY DIFFRACTION100
2.656-2.7490.287710.2281187X-RAY DIFFRACTION100
2.749-2.8520.287580.2141166X-RAY DIFFRACTION100
2.852-2.9690.229600.2071097X-RAY DIFFRACTION100
2.969-3.1010.278740.2071057X-RAY DIFFRACTION100
3.101-3.2520.278630.2151020X-RAY DIFFRACTION100
3.252-3.4270.236520.209972X-RAY DIFFRACTION100
3.427-3.6350.257410.211936X-RAY DIFFRACTION100
3.635-3.8850.208500.2873X-RAY DIFFRACTION100
3.885-4.1960.237430.168823X-RAY DIFFRACTION100
4.196-4.5950.199380.151767X-RAY DIFFRACTION100
4.595-5.1360.229310.144687X-RAY DIFFRACTION100
5.136-5.9270.183260.191641X-RAY DIFFRACTION100
5.927-7.2510.27290.25528X-RAY DIFFRACTION100
7.251-10.2210.309220.291428X-RAY DIFFRACTION100
10.221-46.7641.041100.399255X-RAY DIFFRACTION92.9825

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