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- PDB-1n6f: tricorn protease in complex with Z-Phe-diketo-Arg-Glu-Phe -

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Basic information

Entry
Database: PDB / ID: 1n6f
Titletricorn protease in complex with Z-Phe-diketo-Arg-Glu-Phe
Componentstricorn protease
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 / ClpP/crotonase-like domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 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
Chem-DKT / Tricorn protease
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / direct refinement / Resolution: 2.7 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: Data collection / Database references ...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 / 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 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / pdbx_entry_details ...database_PDB_caveat / pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tricorn protease
B: tricorn protease
C: tricorn protease
D: tricorn protease
E: tricorn protease
F: tricorn protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)735,30912
Polymers730,6776
Non-polymers4,6316
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51260 Å2
ΔGint-125 kcal/mol
Surface area205100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.67, 244.55, 158.32
Angle α, β, γ (deg.)90, 104.59, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tricorn protease


Mass: 121779.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / 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: Chemical
ChemComp-DKT / 4-[2-(3-BENZYLOXYCARBONYLAMINO-4-CYCLOHEXYL-1-HYDROXY-2-OXO-BUTYLAMINO)-5-GUANIDINO-PENTANOYLAMINO]-4-(1-CARBOXY-2-CYCLOHEXYL-ETHYLCARBAMOYL)-BUTYRIC ACID


Mass: 771.900 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H57N7O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.5 %
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: Mar 9, 2002 / 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: 2.7→20 Å / Num. all: 295654 / Num. obs: 178808 / % possible obs: 93.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.65 % / Rsym value: 0.066
Reflection shellResolution: 2.7→2.75 Å / Rsym value: 0.263 / % possible all: 83.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 295654 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 83.6 % / Rmerge(I) obs: 0.263

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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: 2.7→6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 16420 -random
Rwork0.247 ---
obs0.247 148542 85.8 %-
all-164962 --
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49058 0 330 699 50087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONn_bond_d0.012
Refinement
*PLUS
% reflection Rfree: 8.5 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.01

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