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- PDB-1wg0: Structural comparison of Nas6p protein structures in two differen... -

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Basic information

Entry
Database: PDB / ID: 1wg0
TitleStructural comparison of Nas6p protein structures in two different crystal forms
ComponentsProbable 26S proteasome regulatory subunit p28
KeywordsPROTEIN BINDING / Ankyrin repeats / gankyrin homolog / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


proteasome regulatory particle binding / proteasome regulatory particle assembly / nucleus / cytosol
Similarity search - Function
Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Probable 26S proteasome regulatory subunit p28
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsNakamura, Y. / Umehara, T. / Tanaka, A. / Horikoshi, M. / Yokoyama, S. / Padmanabhan, B. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural comparison of Nas6p protein structures in two different crystal forms
Authors: Nakamura, Y. / Umehara, T. / Tanaka, A. / Horikoshi, M. / Yokoyama, S. / Padmanabhan, B.
History
DepositionMay 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Probable 26S proteasome regulatory subunit p28


Theoretical massNumber of molelcules
Total (without water)27,3891
Polymers27,3891
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.444, 68.629, 46.985
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable 26S proteasome regulatory subunit p28 / Proteasome non-ATPase subunit 6 / Nas6p


Mass: 27389.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET28B-NAS6P / Production host: Escherichia coli (E. coli) / References: UniProt: P50086
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 15-20% PEG 4000, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 8677 / Num. obs: 8677 / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.5
Reflection shellResolution: 2.53→2.62 Å / Rmerge(I) obs: 0.191 / % possible all: 93.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IXV

1ixv


Resolution: 2.53→20 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 905 -random
Rwork0.179 ---
all0.182 8451 --
obs0.182 8451 96.3 %-
Displacement parametersBiso mean: 27.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 0 182 2114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.53→2.69 Å
RfactorNum. reflection% reflection
Rfree0.329 146 -
Rwork0.249 --
obs-1134 89 %

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