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- PDB-1pma: PROTEASOME FROM THERMOPLASMA ACIDOPHILUM -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1pma
TitlePROTEASOME FROM THERMOPLASMA ACIDOPHILUM
Components(PROTEASOME) x 2
KeywordsPROTEASE / PROTEASOME / HYDROLASE
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / 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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsLoewe, J. / Stock, D. / Jap, B. / Zwickl, P. / Baumeister, W. / Huber, R.
Citation
Journal: Science / Year: 1995
Title: Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution.
Authors: Lowe, J. / Stock, D. / Jap, B. / Zwickl, P. / Baumeister, W. / Huber, R.
#1: Journal: Science / Year: 1994
Title: Crystal Structure of P22 Tailspike Protein: Interdigitated Subunits in a Thermostable Trimer
Authors: Steinbacher, S. / Seckler, R. / Miller, S. / Steipe, B. / Huber, R. / Reinemer, P.
History
DepositionDec 19, 1994Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASOME
B: PROTEASOME
C: PROTEASOME
D: PROTEASOME
E: PROTEASOME
F: PROTEASOME
G: PROTEASOME
H: PROTEASOME
I: PROTEASOME
J: PROTEASOME
K: PROTEASOME
L: PROTEASOME
M: PROTEASOME
N: PROTEASOME
O: PROTEASOME
P: PROTEASOME
Q: PROTEASOME
R: PROTEASOME
S: PROTEASOME
T: PROTEASOME
U: PROTEASOME
V: PROTEASOME
W: PROTEASOME
X: PROTEASOME
Y: PROTEASOME
Z: PROTEASOME
1: PROTEASOME
2: PROTEASOME


Theoretical massNumber of molelcules
Total (without water)685,99028
Polymers685,99028
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area94960 Å2
ΔGint-210 kcal/mol
Surface area212920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)311.900, 209.700, 117.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PROTEASOME / / PROSOME / MULTICATALYTIC PROTEASE / MCP / MACROPAIN


Mass: 25829.447 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: P25156, EC: 3.4.99.46
#2: Protein
PROTEASOME / / PROSOME / MULTICATALYTIC PROTEASE / MCP / MACROPAIN


Mass: 23169.811 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: P28061, EC: 3.4.99.46

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlproteasomes11
25 mMMPS11
31 mMEDTA11
41 mM11NaN3
510 %PEG100011
60.1 Mpotassium phosphate11
715 %PEG100012
80.1 Mpotassium phosphate12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 105440 / % possible obs: 83 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMV. 5.23data reduction
X-PLOR3.1phasing
RefinementResolution: 3.4→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.221 --
obs0.221 86922 85.7 %
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 3.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56392 0 0 0 56392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.705
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.91
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.498
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_dihedral_angle_d / Dev ideal: 21.916

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