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- PDB-1n6d: Tricorn protease in complex with tetrapeptide chloromethyl ketone... -

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Basic information

Entry
Database: PDB / ID: 1n6d
TitleTricorn protease in complex with tetrapeptide chloromethyl ketone derivative
Components
  • RVRK
  • Tricorn proteaseProteasome endopeptidase complex
KeywordsHYDROLASE / tricorn protease / propeller
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / cytoplasm
Similarity search - Function
Tricorn protease N-terminal domain / Tricorn protease / Tricorn protease, PDZ domain / Tricorn protease PDZ domain / Tricorn protease C1 domain / Tricorn protease C1 domain / Transcription Regulator spoIIAA - #44 / WD40-like beta propeller / WD40-like Beta Propeller Repeat / tail specific protease ...Tricorn protease N-terminal domain / Tricorn protease / Tricorn protease, PDZ domain / Tricorn protease PDZ domain / Tricorn protease C1 domain / Tricorn protease C1 domain / Transcription Regulator spoIIAA - #44 / WD40-like beta propeller / WD40-like Beta Propeller Repeat / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / PDZ domain / Pdz3 Domain / 6 Propeller / Neuraminidase / YVTN repeat-like/Quinoprotein amine dehydrogenase / ClpP/crotonase-like domain superfamily / 7 Propeller / Methylamine Dehydrogenase; Chain H / PDZ superfamily / Roll / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DECANE / Tricorn protease
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / direct refinement / Resolution: 2.8 Å
AuthorsKim, J.-S. / Groll, M. / Huber, R. / Brandstetter, H.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Navigation Inside a Protease: Substrate Selection and Product Exit in the Tricorn Protease from Thermoplasma acidophilum
Authors: Kim, J.-S. / Groll, M. / Musiol, H.-J. / Behrendt, R. / Kaiser, M. / Moroder, L. / Huber, R. / Brandstetter, H.
History
DepositionNov 10, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jan 31, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / 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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tricorn protease
G: RVRK
B: Tricorn protease
H: RVRK
C: Tricorn protease
I: RVRK
D: Tricorn protease
J: RVRK
E: Tricorn protease
K: RVRK
F: Tricorn protease
L: RVRK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)735,09018
Polymers734,23612
Non-polymers8546
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60620 Å2
ΔGint-74 kcal/mol
Surface area207490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.44, 245.43, 159.40
Angle α, β, γ (deg.)90, 104.79, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tricorn protease / Proteasome endopeptidase complex


Mass: 121779.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: tri, Ta1490 / Plasmid: pRSet6c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P96086, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide
RVRK


Mass: 593.186 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: This sequence occurs naturally in thermoplasma acidophilum
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: isopropanol, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
3100 mM1dropNaCl
42 mMbeta-mercaptoethanol1drop
512 %isopropanol1reservoir
6100 mMMES1reservoirpH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 25, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 372512 / Num. obs: 172151 / % possible obs: 88.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.16 % / Rsym value: 0.09
Reflection shellResolution: 2.8→2.84 Å / Rsym value: 0.393 / % possible all: 87
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 372512 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 87 % / Rmerge(I) obs: 0.393

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: direct refinement
Starting model: PDB ENTRY 1K32

1k32


Resolution: 2.8→6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.315 15317 -random
Rwork0.285 ---
obs0.285 138672 88.7 %-
all-153989 --
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49290 0 66 534 49890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONn_bond_d0.034
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 8.8 % / Rfactor Rwork: 0.284
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.009

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