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- PDB-3h43: N-terminal domain of the proteasome-activating nucleotidase of Me... -

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Basic information

Entry
Database: PDB / ID: 3h43
TitleN-terminal domain of the proteasome-activating nucleotidase of Methanocaldococcus jannaschii
ComponentsProteasome-activating nucleotidase
KeywordsHYDROLASE / Proteasome / regulatory particle / nucleosidase / ATP-binding / Cytoplasm / Nucleotide-binding
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / CTPase activity / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasomal protein catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / GTPase activity ...proteasome-activating nucleotidase complex / CTPase activity / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasomal protein catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / GTPase activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
Proteasome-activating nucleotidase PAN / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities ...Proteasome-activating nucleotidase PAN / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proteasome-activating nucleotidase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJeffrey, P.D. / Zhang, F. / Hu, M. / Tian, G. / Zhang, P. / Finley, D. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Insights into the Regulatory Particle of the Proteasome from Methanocaldococcus jannaschii.
Authors: Zhang, F. / Hu, M. / Tian, G. / Zhang, P. / Finley, D. / Jeffrey, P.D. / Shi, Y.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome-activating nucleotidase
B: Proteasome-activating nucleotidase
C: Proteasome-activating nucleotidase
D: Proteasome-activating nucleotidase
E: Proteasome-activating nucleotidase
F: Proteasome-activating nucleotidase
G: Proteasome-activating nucleotidase
H: Proteasome-activating nucleotidase
I: Proteasome-activating nucleotidase
J: Proteasome-activating nucleotidase
K: Proteasome-activating nucleotidase
L: Proteasome-activating nucleotidase


Theoretical massNumber of molelcules
Total (without water)117,08412
Polymers117,08412
Non-polymers00
Water2,396133
1
A: Proteasome-activating nucleotidase
B: Proteasome-activating nucleotidase
E: Proteasome-activating nucleotidase
F: Proteasome-activating nucleotidase
I: Proteasome-activating nucleotidase
J: Proteasome-activating nucleotidase


Theoretical massNumber of molelcules
Total (without water)58,5426
Polymers58,5426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-72 kcal/mol
Surface area24200 Å2
MethodPISA
2
C: Proteasome-activating nucleotidase
D: Proteasome-activating nucleotidase
G: Proteasome-activating nucleotidase
H: Proteasome-activating nucleotidase
K: Proteasome-activating nucleotidase
L: Proteasome-activating nucleotidase


Theoretical massNumber of molelcules
Total (without water)58,5426
Polymers58,5426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-67 kcal/mol
Surface area24570 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24890 Å2
ΔGint-156 kcal/mol
Surface area42000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.640, 129.620, 60.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsAuthor states that dodecamer is not biologically relevant and is the result of crystal packing.

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Components

#1: Protein
Proteasome-activating nucleotidase / Proteasome regulatory subunit


Mass: 9756.964 Da / Num. of mol.: 12 / Fragment: N-terminal domain (74-150)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: pan, MJ1176 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q58576
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M NaOAc, pH 4.5, 0.2 M Li2SO4and 34%-36% MPD (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791, 0.9792, 0.9641
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2007
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97921
30.96411
ReflectionResolution: 2.1→100 Å / Num. all: 58671 / Num. obs: 58671 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.093
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Num. unique all: 5345 / Rsym value: 0.426 / % possible all: 91.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→40.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2883633.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2931 5 %RANDOM
Rwork0.217 ---
all0.223 58361 --
obs0.217 58361 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3292 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å20 Å20 Å2
2---3.53 Å20 Å2
3---7.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7179 0 0 133 7312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 475 5.2 %
Rwork0.238 8606 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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