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- PDB-4hwy: Trypanosoma brucei procathepsin B solved from 40 fs free-electron... -

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Basic information

Entry
Database: PDB / ID: 4hwy
TitleTrypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by serial femtosecond X-ray crystallography
ComponentsCysteine peptidase C (CPC)
KeywordsHYDROLASE / Papain fold / Lysosomal cysteine protease
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 / 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 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
Cysteine peptidase C (CPC)
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRedecke, L. / Nass, K. / DePonte, D.P. / White, T.A. / Rehders, D. / Barty, A. / Stellato, F. / Liang, M. / Barends, T.R.M. / Boutet, S. ...Redecke, L. / Nass, K. / DePonte, D.P. / White, T.A. / Rehders, D. / Barty, A. / Stellato, F. / Liang, M. / Barends, T.R.M. / Boutet, S. / Williams, G.W. / Messerschmidt, M. / Seibert, M.M. / Aquila, A. / Arnlund, D. / Bajt, S. / Barth, T. / Bogan, M.J. / Caleman, C. / Chao, T.-C. / Doak, R.B. / Fleckenstein, H. / Frank, M. / Fromme, R. / Galli, L. / Grotjohann, I. / Hunter, M.S. / Johansson, L.C. / Kassemeyer, S. / Katona, G. / Kirian, R.A. / Koopmann, R. / Kupitz, C. / Lomb, L. / Martin, A.V. / Mogk, S. / Neutze, R. / Shoemann, R.L. / Steinbrener, J. / Timneanu, N. / Wang, D. / Weierstall, U. / Zatsepin, N.A. / Spence, J.C.H. / Fromme, P. / Schlichting, I. / Duszenko, M. / Betzel, C. / Chapman, H.
CitationJournal: Science / Year: 2013
Title: Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.
Authors: Redecke, L. / Nass, K. / DePonte, D.P. / White, T.A. / Rehders, D. / Barty, A. / Stellato, F. / Liang, M. / Barends, T.R. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / Seibert, M.M. / ...Authors: Redecke, L. / Nass, K. / DePonte, D.P. / White, T.A. / Rehders, D. / Barty, A. / Stellato, F. / Liang, M. / Barends, T.R. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / Seibert, M.M. / Aquila, A. / Arnlund, D. / Bajt, S. / Barth, T. / Bogan, M.J. / Caleman, C. / Chao, T.C. / Doak, R.B. / Fleckenstein, H. / Frank, M. / Fromme, R. / Galli, L. / Grotjohann, I. / Hunter, M.S. / Johansson, L.C. / Kassemeyer, S. / Katona, G. / Kirian, R.A. / Koopmann, R. / Kupitz, C. / Lomb, L. / Martin, A.V. / Mogk, S. / Neutze, R. / Shoeman, R.L. / Steinbrener, J. / Timneanu, N. / Wang, D. / Weierstall, U. / Zatsepin, N.A. / Spence, J.C. / Fromme, P. / Schlichting, I. / Duszenko, M. / Betzel, C. / Chapman, H.N.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Dec 21, 2016Group: Data collection
Revision 1.4Nov 15, 2017Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.5Feb 14, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
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 / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.occupancy / _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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,2713
Polymers37,2601
Non-polymers1,0112
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.400, 125.400, 54.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-590-

HOH

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Components

#1: Protein Cysteine peptidase C (CPC)


Mass: 37259.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb927.6.560 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: D6XHE1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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-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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 293195

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 310.15 K
Method: crystallization in vivo within living sf9 insect cells
pH: 7.4
Details: Spontaneous formation of needle-shaped microcrystals in Sf9 cells infected with recombinant baculovirus containing the gene encoding the pre-pro form of Trypanosoma brucei cathepsin B, pH 7. ...Details: Spontaneous formation of needle-shaped microcrystals in Sf9 cells infected with recombinant baculovirus containing the gene encoding the pre-pro form of Trypanosoma brucei cathepsin B, pH 7.4, Crystallization in vivo within living SF9 insect cells, temperature 310.15K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.32 Å
DetectorType: Cornell-SLAC Pixel Array Detector / Detector: PIXEL / Date: Feb 1, 2011
RadiationMonochromator: CXI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 25969 / Num. obs: 25969 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.175 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CXIDAQdata collection
MOLREPphasing
REFMAC5.6.0117refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MOR

3mor


Resolution: 2.1→88.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.531 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21308 1321 5.1 %RANDOM
Rwork0.18181 ---
obs0.18335 24648 99.99 %-
all-24648 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.244 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→88.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 67 98 2551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022486
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9523396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2523.661112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67115329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7731513
X-RAY DIFFRACTIONr_chiral_restr0.1220.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211965
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 90 -
Rwork0.317 1612 -
obs--100 %

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