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- PDB-3q5w: Structure of proteasome tether -

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Basic information

Entry
Database: PDB / ID: 3q5w
TitleStructure of proteasome tether
ComponentsProtein cut8
KeywordsCELL CYCLE / PROTEASOME / TETHER / 26S / CHROMOSOME / dimer / novel fold
Function / homology
Function and homology information


proteasome localization / sterol binding / nuclear protein quality control by the ubiquitin-proteasome system / proteasome binding / nuclear periphery / nuclear envelope / chromatin / identical protein binding / nucleus
Similarity search - Function
Tethering factor for nuclear proteasome Cut8/Sts1 / Tethering factor for nuclear proteasome Cut8/Sts1 / Cut8/Sts1 superfamily / Cut8, nuclear proteasome tether protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tethering factor for nuclear proteasome cut8
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsSchumacher, M.A.
CitationJournal: To be Published
Title: Structure of Proteasome Tether
Authors: Schumacher, M.A. / Glover, T. / Weijun, X.
History
DepositionDec 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein cut8
B: Protein cut8


Theoretical massNumber of molelcules
Total (without water)57,4902
Polymers57,4902
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-40 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.660, 51.180, 71.330
Angle α, β, γ (deg.)103.92, 100.02, 98.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein cut8 / Cell untimely torn protein 8


Mass: 28744.807 Da / Num. of mol.: 2 / Fragment: UNP residues 1-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cut8, SPAC17C9.13c / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38937
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: TASCIMATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9790, 0.9780, 0.939
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2008 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9781
30.9391
ReflectionResolution: 2.75→67.6 Å / Num. obs: 11764 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.07 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.75→67.6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 569003.4 / 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
Rfree0.276 1039 8.8 %RANDOM
Rwork0.231 ---
obs0.231 11764 95.8 %-
all-12280 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.7139 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 72.5 Å2
Baniso -1Baniso -2Baniso -3
1-15.9 Å216.05 Å2-3.04 Å2
2---1.94 Å211.84 Å2
3----13.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.75→67.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 0 13 3239
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.261.5
X-RAY DIFFRACTIONc_mcangle_it6.432
X-RAY DIFFRACTIONc_scbond_it6.812
X-RAY DIFFRACTIONc_scangle_it9.462.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 169 8.8 %
Rwork0.311 1755 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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