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- PDB-2z5e: Crystal Structure of Proteasome Assembling Chaperone 3 -

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Basic information

Entry
Database: PDB / ID: 2z5e
TitleCrystal Structure of Proteasome Assembling Chaperone 3
ComponentsProteasome Assembling Chaperone 3
KeywordsCHAPERONE / BETA SANDWICH / HOMODIMER / PROTEASOME
Function / homology
Function and homology information


chaperone-mediated protein complex assembly / proteasome assembly / molecular adaptor activity / protein-containing complex binding / protein-containing complex
Similarity search - Function
Ribosomal Protein S5; domain 2 - #90 / Proteasome assembly chaperone 3 / : / Proteasome assembly chaperone 3 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome assembly chaperone 3 / Proteasome assembly chaperone 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsOkamoto, K. / Kurimoto, E. / Sakata, E. / Suzuki, A. / Yamane, T. / Hirano, Y. / Murata, S. / Tanaka, K. / Kato, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes
Authors: Yashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Niwa, S. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Takagi, K. / Suzuki, A. / Hirano, Y. / ...Authors: Yashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Niwa, S. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Takagi, K. / Suzuki, A. / Hirano, Y. / Murata, S. / Kato, K. / Yamane, T. / Tanaka, K.
History
DepositionJul 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome Assembling Chaperone 3
B: Proteasome Assembling Chaperone 3


Theoretical massNumber of molelcules
Total (without water)26,2372
Polymers26,2372
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-25.6 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.642, 88.642, 57.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Proteasome Assembling Chaperone 3 / Hypothetical protein MGC10911


Mass: 13118.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSF-Duet I / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4D216, UniProt: Q9BT73*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30%(w/v) PEG4000, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 25, 2006
RadiationMonochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→62.99 Å / Num. all: 15971 / Num. obs: 15971 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.452 / Num. unique all: 1574 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→27.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.407 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25221 793 5 %RANDOM
Rwork0.18016 ---
all0.1836 15135 --
obs0.1836 15135 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.097 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.193 Å0.209 Å
Refinement stepCycle: LAST / Resolution: 2→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 0 255 2138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221915
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9882617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52425.59359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0615358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.874156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021346
X-RAY DIFFRACTIONr_nbd_refined0.2120.2917
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.221
X-RAY DIFFRACTIONr_mcbond_it1.2021.51292
X-RAY DIFFRACTIONr_mcangle_it1.91322060
X-RAY DIFFRACTIONr_scbond_it2.7913692
X-RAY DIFFRACTIONr_scangle_it4.474.5552
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 69 -
Rwork0.189 1084 -
obs-1084 100 %

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