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- PDB-1j2q: 20S proteasome in complex with calpain-Inhibitor I from archaeogl... -

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Basic information

Entry
Database: PDB / ID: 1j2q
Title20S proteasome in complex with calpain-Inhibitor I from archaeoglobus fulgidus
Components
  • Proteasome alpha subunit
  • Proteasome beta subunit
KeywordsHYDROLASE / proteasome / ubiquitin / 20S / CP
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain ...Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CIB / Proteasome subunit alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsGroll, M. / Brandstetter, H. / Bartunik, H. / Bourenkow, G. / Huber, R.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Investigations on the Maturation and Regulation of Archaebacterial Proteasomes
Authors: Groll, M. / Brandstetter, H. / Bartunik, H. / Bourenkow, G. / Huber, R.
History
DepositionJan 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_sheet / 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_sheet.number_strands / _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: pdbx_entry_details / 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: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,54121
Polymers340,85714
Non-polymers2,6857
Water1,892105
1
A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
hetero molecules

A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)687,08342
Polymers681,71328
Non-polymers5,36914
Water50428
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area109540 Å2
ΔGint-262 kcal/mol
Surface area215580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)148.097, 148.097, 303.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the bioogical assembly is generated by the two-fold axis: x, -y, -z+2/3

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Components

#1: Protein
Proteasome alpha subunit


Mass: 26561.521 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: prset6c / Production host: Escherichia coli (E. coli)
References: UniProt: O29760, proteasome endopeptidase complex
#2: Protein
Proteasome beta subunit


Mass: 22132.283 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: prset6c / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P996, proteasome endopeptidase complex
#3: Chemical
ChemComp-CIB / 2-ACETYLAMINO-4-METHYL-PENTANOIC ACID [1-(1-FORMYL-PENTYLCARBAMOYL)-3-METHYL-BUTYL]-AMIDE / CALPAIN IHIBITOR I


Mass: 383.525 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C20H37N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 9% PEG 400, 80mM MgCl2, 100mM NaAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 24 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
2100 mM1reservoirpH4.6NaOAc
39 %(w/v)PEG4001reservoir
480 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 87322 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 46.1 Å2
Reflection shellResolution: 2.83→2.88 Å / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 1140521 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Rmerge(I) obs: 0.399

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→16.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3321738.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 4404 5.1 %RANDOM
Rwork0.241 ---
all0.243 87104 --
obs0.243 87104 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.0264 Å2 / ksol: 0.307215 e/Å3
Displacement parametersBiso mean: 51.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å21.35 Å20 Å2
2---3.8 Å20 Å2
3---7.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.83→16.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23933 0 189 105 24227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.83→2.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 609 5 %
Rwork0.383 11521 -
obs--77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CAL.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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