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- PDB-1ixv: Crystal Structure Analysis of homolog of oncoprotein gankyrin, an... -

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Basic information

Entry
Database: PDB / ID: 1ixv
TitleCrystal Structure Analysis of homolog of oncoprotein gankyrin, an interactor of Rb and CDK4/6
ComponentsProbable 26S proteasome regulatory subunit p28
KeywordsPROTEIN BINDING / Ankyrin repeats
Function / homology
Function and homology information


proteasome regulatory particle binding / proteasome regulatory particle assembly / protein folding chaperone / 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 / MIR / Resolution: 2.3 Å
AuthorsPadmanabhan, B. / Adachi, N. / Kataoka, K. / Horikoshi, M.
CitationJournal: J.BIOL.CHEM. / Year: 2004
Title: Crystal structure of the homolog of the oncoprotein gankyrin, an interactor of Rb and CDK4/6
Authors: Padmanabhan, B. / Adachi, N. / Kataoka, K. / Horikoshi, M.
History
DepositionJul 9, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)25,9341
Polymers25,9341
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.433, 61.736, 98.095
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 Probable 26S proteasome regulatory subunit p28


Mass: 25933.566 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.: 102 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Adachi, N., (2002) Acta Cryst., D58, 859.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
215-20 %PEG40001reservoir
30.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 11582 / Num. obs: 11582 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.46 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SCALAdata scaling
SOLVEphasing
CCP4model building
CNS1refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→29.45 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 588 5.1 %RANDOM
Rwork0.194 ---
all0.198 11582 --
obs-11582 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.2048 Å2 / ksol: 0.341422 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2--2.16 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 0 102 1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 87 4.7 %
Rwork0.222 1779 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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