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- PDB-3mor: Crystal structure of Cathepsin B from Trypanosoma Brucei -

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Basic information

Entry
Database: PDB / ID: 3mor
TitleCrystal structure of Cathepsin B from Trypanosoma Brucei
ComponentsCathepsin B-like cysteine protease
KeywordsHYDROLASE / Thiol Protease
Function / homology
Function and homology information


post-transcriptional regulation of gene expression / cysteine-type peptidase activity / proteolysis / metal ion binding
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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A ...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
Cathepsin B-like cysteine protease
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCupelli, K. / Stehle, T.
CitationJournal: Nat.Methods / Year: 2012
Title: In vivo protein crystallization opens new routes in structural biology.
Authors: Koopmann, R. / Cupelli, K. / Redecke, L. / Nass, K. / Deponte, D.P. / White, T.A. / Stellato, F. / Rehders, D. / Liang, M. / Andreasson, J. / Aquila, A. / Bajt, S. / Barthelmess, M. / Barty, ...Authors: Koopmann, R. / Cupelli, K. / Redecke, L. / Nass, K. / Deponte, D.P. / White, T.A. / Stellato, F. / Rehders, D. / Liang, M. / Andreasson, J. / Aquila, A. / Bajt, S. / Barthelmess, M. / Barty, A. / Bogan, M.J. / Bostedt, C. / Boutet, S. / Bozek, J.D. / Caleman, C. / Coppola, N. / Davidsson, J. / Doak, R.B. / Ekeberg, T. / Epp, S.W. / Erk, B. / Fleckenstein, H. / Foucar, L. / Graafsma, H. / Gumprecht, L. / Hajdu, J. / Hampton, C.Y. / Hartmann, A. / Hartmann, R. / Hauser, G. / Hirsemann, H. / Holl, P. / Hunter, M.S. / Kassemeyer, S. / Kirian, R.A. / Lomb, L. / Maia, F.R. / Kimmel, N. / Martin, A.V. / Messerschmidt, M. / Reich, C. / Rolles, D. / Rudek, B. / Rudenko, A. / Schlichting, I. / Schulz, J. / Seibert, M.M. / Shoeman, R.L. / Sierra, R.G. / Soltau, H. / Stern, S. / Struder, L. / Timneanu, N. / Ullrich, J. / Wang, X. / Weidenspointner, G. / Weierstall, U. / Williams, G.J. / Wunderer, C.B. / Fromme, P. / Spence, J.C. / Stehle, T. / Chapman, H.N. / Betzel, C. / Duszenko, M.
History
DepositionApr 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin B-like cysteine protease
B: Cathepsin B-like cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,24613
Polymers69,7642
Non-polymers1,48311
Water97354
1
A: Cathepsin B-like cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6056
Polymers34,8821
Non-polymers7245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin B-like cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6417
Polymers34,8821
Non-polymers7596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.910, 75.490, 75.600
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPROAA80 - 9557 - 72
21LEULEUPROPROBB80 - 9557 - 72
12ALAALAASPASPAA103 - 11580 - 92
22ALAALAASPASPBB103 - 11580 - 92
13CYSCYSTRPTRPAA119 - 12396 - 100
23CYSCYSTRPTRPBB119 - 12396 - 100
14ALAALAASPASPAA127 - 133104 - 110
24ALAALAASPASPBB127 - 133104 - 110
15VALVALSERSERAA144 - 193121 - 170
25VALVALSERSERBB144 - 193121 - 170
16PROPROCYSCYSAA203 - 215180 - 192
26PROPROCYSCYSBB203 - 215180 - 192
17CYSCYSPROPROAA219 - 334196 - 311
27CYSCYSPROPROBB219 - 334196 - 311

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Cathepsin B-like cysteine protease / Cysteine peptidase C (CPC)


Mass: 34881.789 Da / Num. of mol.: 2 / Fragment: Residues 24-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb927.6.560 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q6R7Z5, 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 63 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350,(NH4)2HPO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2010
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→48 Å / Num. obs: 34696 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rsym value: 0.292 / Net I/σ(I): 6.99
Reflection shellResolution: 2.55→2.67 Å / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QDQ

1qdq


Resolution: 2.55→48 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.854 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.583 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 1.012 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24299 959 5.1 %RANDOM
Rwork0.20235 ---
obs0.20445 17772 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.998 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.61 Å2
2---0.51 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 95 54 4140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214249
X-RAY DIFFRACTIONr_bond_other_d0.0020.028
X-RAY DIFFRACTIONr_angle_refined_deg0.61.9455803
X-RAY DIFFRACTIONr_angle_other_deg0.368316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56923.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53115551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1871522
X-RAY DIFFRACTIONr_chiral_restr0.0490.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213406
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8241.52596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56224153
X-RAY DIFFRACTIONr_scbond_it2.44231653
X-RAY DIFFRACTIONr_scangle_it3.8684.51650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1696 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.195
LOOSE THERMAL1.4410
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 58 -
Rwork0.27 1347 -
obs--98.25 %

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