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- PDB-1q5q: The Rhodococcus 20S proteasome -

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Basic information

Entry
Database: PDB / ID: 1q5q
TitleThe Rhodococcus 20S proteasome
Components
  • proteasome alpha-type subunit 1
  • proteasome beta-type subunit 1
KeywordsHYDROLASE / proteasome assembly / pro-peptide / inter-subunit contacts / Rhodococcus erythropolis
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 / modification-dependent protein catabolic process / endopeptidase activity / cytoplasm
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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
Proteasome subunit beta 1 / Proteasome subunit alpha 1
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKwon, Y.D. / Nagy, I. / Adams, P.D. / Baumeister, W. / Jap, B.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly.
Authors: Kwon, Y.D. / Nagy, I. / Adams, P.D. / Baumeister, W. / Jap, B.K.
History
DepositionAug 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: proteasome alpha-type subunit 1
B: proteasome alpha-type subunit 1
C: proteasome alpha-type subunit 1
D: proteasome alpha-type subunit 1
E: proteasome alpha-type subunit 1
F: proteasome alpha-type subunit 1
G: proteasome alpha-type subunit 1
H: proteasome beta-type subunit 1
I: proteasome beta-type subunit 1
J: proteasome beta-type subunit 1
K: proteasome beta-type subunit 1
L: proteasome beta-type subunit 1
M: proteasome beta-type subunit 1
N: proteasome beta-type subunit 1


Theoretical massNumber of molelcules
Total (without water)373,32114
Polymers373,32114
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: proteasome alpha-type subunit 1
B: proteasome alpha-type subunit 1
C: proteasome alpha-type subunit 1
D: proteasome alpha-type subunit 1
E: proteasome alpha-type subunit 1
F: proteasome alpha-type subunit 1
G: proteasome alpha-type subunit 1
H: proteasome beta-type subunit 1
I: proteasome beta-type subunit 1
J: proteasome beta-type subunit 1
K: proteasome beta-type subunit 1
L: proteasome beta-type subunit 1
M: proteasome beta-type subunit 1
N: proteasome beta-type subunit 1

A: proteasome alpha-type subunit 1
B: proteasome alpha-type subunit 1
C: proteasome alpha-type subunit 1
D: proteasome alpha-type subunit 1
E: proteasome alpha-type subunit 1
F: proteasome alpha-type subunit 1
G: proteasome alpha-type subunit 1
H: proteasome beta-type subunit 1
I: proteasome beta-type subunit 1
J: proteasome beta-type subunit 1
K: proteasome beta-type subunit 1
L: proteasome beta-type subunit 1
M: proteasome beta-type subunit 1
N: proteasome beta-type subunit 1


Theoretical massNumber of molelcules
Total (without water)746,64228
Polymers746,64228
Non-polymers00
Water50428
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area75580 Å2
ΔGint-35 kcal/mol
Surface area231590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)150.112, 215.307, 251.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
proteasome alpha-type subunit 1


Mass: 28346.840 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: BL21 / Gene: PRCA(1) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53080, proteasome endopeptidase complex
#2: Protein
proteasome beta-type subunit 1


Mass: 24984.766 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: BL21 / Gene: PRCB(1) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53079
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 14% PEG 6000, 50mM sodium citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
210 mMTris-HCl1droppH7.0
314 %(w/v)PEG60001reservoir
450 mMsodium citrate1reservoirpH5.4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 114039 / Observed criterion σ(I): 0 / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.074
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 91.7 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PMA

1pma


Resolution: 2.6→19.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 183405.38 / Data cutoff high rms absF: 183405.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 11414 10 %RANDOM
Rwork0.246 ---
obs0.246 113989 91.7 %-
all-124455 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.7308 Å2 / ksol: 0.312508 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å20 Å20 Å2
2--2.48 Å20 Å2
3----7.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23539 0 0 167 23706
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.882.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 1499 9.8 %
Rwork0.319 13768 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. reflection obs: 113987
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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