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- PDB-2vt8: Structure of a conserved dimerisation domain within Fbox7 and PI31 -

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Basic information

Entry
Database: PDB / ID: 2vt8
TitleStructure of a conserved dimerisation domain within Fbox7 and PI31
ComponentsPROTEASOME INHIBITOR PI31 SUBUNIT
KeywordsHYDROLASE INHIBITOR / POLYMORPHISM
Function / homology
Function and homology information


negative regulation of proteasomal protein catabolic process / Proteasome assembly / proteasome core complex / endopeptidase inhibitor activity / proteasome binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein heterodimerization activity / perinuclear region of cytoplasm / endoplasmic reticulum ...negative regulation of proteasomal protein catabolic process / Proteasome assembly / proteasome core complex / endopeptidase inhibitor activity / proteasome binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein heterodimerization activity / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / membrane / cytosol
Similarity search - Function
Protein Transport Mog1p; Chain A - #30 / Proteasome inhibitor PI31-like / PI31 proteasome regulator, C-terminal / PI31 proteasome regulator, N-terminal / PI31 proteasome regulator / PI31 proteasome regulator N-terminal / Protein Transport Mog1p; Chain A / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome inhibitor PI31 subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKirk, R.J. / Murray-Rust, J. / Knowles, P.P. / Laman, H. / McDonald, N.Q.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of a Conserved Dimerization Domain within the F-Box Protein Fbxo7 and the Pi31 Proteasome Inhibitor.
Authors: Kirk, R.J. / Laman, H. / Knowles, P.P. / Murray-Rust, J. / Lomonosov, M. / Meziane, E.K. / McDonald, N.Q.
History
DepositionMay 12, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Mar 7, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASOME INHIBITOR PI31 SUBUNIT
B: PROTEASOME INHIBITOR PI31 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)34,3972
Polymers34,3972
Non-polymers00
Water64936
1
A: PROTEASOME INHIBITOR PI31 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)17,1981
Polymers17,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEASOME INHIBITOR PI31 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)17,1981
Polymers17,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.498, 45.212, 67.279
Angle α, β, γ (deg.)90.00, 111.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9756, 0.03852, 0.2162), (0.08253, -0.8478, 0.5239), (0.2035, 0.5289, 0.8239)
Vector: 72.19, 24.38, -15.35)

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Components

#1: Protein PROTEASOME INHIBITOR PI31 SUBUNIT / HPI31 / PI31


Mass: 17198.361 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-151 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92530
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 36 TO CSO ENGINEERED RESIDUE IN CHAIN B, PHE 36 TO CSO
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 8 / Details: 20% PEG 3350, 0.1 M AMMONIUM IODIDE, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 6, 2004 / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→28.1 Å / Num. obs: 9607 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PART-REFINED MODEL OF A L7M SEMET DERIVATIVE OBTAINED BY SAD PHASING

Resolution: 2.6→28.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.888 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 1.262 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 459 4.8 %RANDOM
Rwork0.203 ---
obs0.206 9115 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.2 Å2
2--0.53 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 0 36 2180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.962984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg23.6885.275291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36824.39691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20215320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.781159
X-RAY DIFFRACTIONr_chiral_restr0.1350.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2895
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21440
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.481.51457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13122245
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6763821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7484.5739
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.406 30
Rwork0.295 648

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