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- PDB-1k32: Crystal structure of the tricorn protease -

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Basic information

Entry
Database: PDB / ID: 1k32
TitleCrystal structure of the tricorn protease
Componentstricorn proteaseProteasome endopeptidase complex
KeywordsHYDROLASE / protein degradation / substrate gating / serine protease / beta propeller / proteasome
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
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD, NCS Averaging / Resolution: 2 Å
AuthorsBrandstetter, H. / Kim, J.-S. / Groll, M. / Huber, R.
CitationJournal: Nature / Year: 2001
Title: Crystal structure of the tricorn protease reveals a protein disassembly line.
Authors: Brandstetter, H. / Kim, J.S. / Groll, M. / Huber, R.
History
DepositionOct 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN HOH 2001-2399 ARE ASSOCIATED WITH CHAIN A. HOH 3001-3399 ARE ASSOCIATED WITH CHAIN B. HOH ...HETEROGEN HOH 2001-2399 ARE ASSOCIATED WITH CHAIN A. HOH 3001-3399 ARE ASSOCIATED WITH CHAIN B. HOH 4001-4399 ARE ASSOCIATED WITH CHAIN C. HOH 5001-5399 ARE ASSOCIATED WITH CHAIN D. HOH 6001-6399 ARE ASSOCIATED WITH CHAIN E. HOH 7001-7399 ARE ASSOCIATED WITH CHAIN F.

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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


Theoretical massNumber of molelcules
Total (without water)712,0806
Polymers712,0806
Non-polymers00
Water43,1282394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52130 Å2
ΔGint-128 kcal/mol
Surface area207920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.86, 245.998, 159.04
Angle α, β, γ (deg.)90.0, 105.296, 90.0
Int Tables number4
Space group name H-MP1211
Detailshomohexamer following 3-2 symmetry, completely contained in the coordinate file

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Components

#1: Protein
tricorn protease / Proteasome endopeptidase complex


Mass: 118680.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA1490 / Plasmid: pRSET-tric / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P96086, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2394 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% isopropanol, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
225-30 %MES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 475881 / Num. obs: 394093 / % possible obs: 82.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 1.9 / Num. unique all: 394093 / Rsym value: 0.313 / % possible all: 68.1
Reflection
*PLUS
Rmerge(I) obs: 0.208
Reflection shell
*PLUS
Rmerge(I) obs: 0.313

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Processing

Software
NameVersionClassification
RSPSmodel building
MLPHAREphasing
MAINmodel building
SOLOMONphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RSPSphasing
MAINphasing
RefinementMethod to determine structure: MIR, MAD, NCS Averaging / Resolution: 2→20 Å
Cross valid method: direct space free density correlation reciprocal free R
σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 19824 5.3 %5%
Rwork0.245 ---
all-374269 --
obs-374269 78.6 %-
Displacement parametersBiso mean: 30.74 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49062 0 0 2394 51456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.34
LS refinement shellResolution: 2→2.04 Å
RfactorNum. reflection% reflection
Rfree0.323 1438 4.5 %
Rwork0.289 --
obs-31827 79.1 %
Refinement
*PLUS
Rfactor obs: 0.248 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.08
X-RAY DIFFRACTIONc_angle_d1
LS refinement shell
*PLUS
Rfactor Rfree: 0.323 / Rfactor Rwork: 0.289

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