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- PDB-7e3f: Crystal structure of Trypanosoma brucei cathepsin B Y217C/S275C mutant -

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Basic information

Entry
Database: PDB / ID: 7e3f
TitleCrystal structure of Trypanosoma brucei cathepsin B Y217C/S275C 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: 2.35 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,3933
Polymers34,3821
Non-polymers1,0112
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint16 kcal/mol
Surface area14120 Å2
Unit cell
Length a, b, c (Å)123.650, 123.650, 54.280
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: 34382.277 Da / Num. of mol.: 1 / Mutation: Y217C, S275C
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.: 36 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
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: 2.35→50 Å / Num. obs: 18117 / % possible obs: 100 % / Redundancy: 243 % / CC1/2: 0.979 / Net I/σ(I): 6.9
Reflection shellResolution: 2.35→2.37 Å / Num. unique obs: 445 / CC1/2: 0.416

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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: 2.35→49.751 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.383 / SU ML: 0.187 / Cross valid method: FREE R-VALUE / ESU R: 0.307 / ESU R Free: 0.234
RfactorNum. reflection% reflection
Rfree0.2572 922 5.1 %
Rwork0.2189 17158 -
all0.221 --
obs-18080 99.978 %
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: 30.125 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2--1.22 Å20 Å2
3----2.439 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 67 36 2482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132528
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172148
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6823451
X-RAY DIFFRACTIONr_angle_other_deg1.2371.6135008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3085306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5621.94134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22115353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5741516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022870
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_nbd_refined0.180.2396
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.21874
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21168
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2870.215
X-RAY DIFFRACTIONr_nbd_other0.190.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.27
X-RAY DIFFRACTIONr_mcbond_it2.1883.0361230
X-RAY DIFFRACTIONr_mcbond_other2.1873.0341229
X-RAY DIFFRACTIONr_mcangle_it3.4544.541534
X-RAY DIFFRACTIONr_mcangle_other3.4544.5421535
X-RAY DIFFRACTIONr_scbond_it3.0123.4421298
X-RAY DIFFRACTIONr_scbond_other3.0123.4421298
X-RAY DIFFRACTIONr_scangle_it4.7245.0331917
X-RAY DIFFRACTIONr_scangle_other4.7235.0351918
X-RAY DIFFRACTIONr_lrange_it5.88934.0142603
X-RAY DIFFRACTIONr_lrange_other5.8934.0082603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.407720.3411226X-RAY DIFFRACTION100
2.411-2.4770.352520.3171228X-RAY DIFFRACTION100
2.477-2.5490.364620.3071169X-RAY DIFFRACTION100
2.549-2.6270.323690.2851140X-RAY DIFFRACTION100
2.627-2.7130.315710.2451110X-RAY DIFFRACTION100
2.713-2.8080.25530.2191077X-RAY DIFFRACTION100
2.808-2.9140.231540.2081042X-RAY DIFFRACTION100
2.914-3.0330.258750.208993X-RAY DIFFRACTION100
3.033-3.1680.261520.219976X-RAY DIFFRACTION100
3.168-3.3220.24450.208912X-RAY DIFFRACTION100
3.322-3.5020.249530.209883X-RAY DIFFRACTION100
3.502-3.7140.215420.209845X-RAY DIFFRACTION100
3.714-3.970.2460.203793X-RAY DIFFRACTION100
3.97-4.2870.23340.175746X-RAY DIFFRACTION100
4.287-4.6950.128340.135697X-RAY DIFFRACTION100
4.695-5.2470.261290.147626X-RAY DIFFRACTION100
5.247-6.0550.22200.185582X-RAY DIFFRACTION100
6.055-7.4070.233290.246479X-RAY DIFFRACTION100
7.407-10.4380.309200.273392X-RAY DIFFRACTION100
10.438-49.70.67100.452242X-RAY DIFFRACTION98.4375

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