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- PDB-2ppi: Structure of the BTB (Tramtrack and Bric a brac) domain of human ... -

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Basic information

Entry
Database: PDB / ID: 2ppi
TitleStructure of the BTB (Tramtrack and Bric a brac) domain of human Gigaxonin
ComponentsGigaxonin
KeywordsSTRUCTURAL PROTEIN / BTB domain / protein degradation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Cul3-RING ubiquitin ligase complex / cytoskeleton organization / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cytoskeleton / protein ubiquitination / cytosol / cytoplasm
Similarity search - Function
Gigaxonin / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch motif ...Gigaxonin / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAmos, A. / Turnbull, A.P. / Tickle, J. / Keates, T. / Bullock, A. / Savitsky, P. / Burgess-Brown, N. / Debreczeni, J.E. / Ugochukwu, E. / Umeano, C. ...Amos, A. / Turnbull, A.P. / Tickle, J. / Keates, T. / Bullock, A. / Savitsky, P. / Burgess-Brown, N. / Debreczeni, J.E. / Ugochukwu, E. / Umeano, C. / Pike, A.C.W. / Papagrigoriou, E. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of the BTB (Tramtrack and Bric a brac) domain of human Gigaxonin.
Authors: Amos, A. / Turnbull, A.P. / Tickle, J. / Keates, T. / Bullock, A. / Savitsky, P. / Burgess-Brown, N. / Debreczeni, J.E. / Ugochukwu, E. / Umeano, C. / Pike, A.C.W. / Papagrigoriou, E. / ...Authors: Amos, A. / Turnbull, A.P. / Tickle, J. / Keates, T. / Bullock, A. / Savitsky, P. / Burgess-Brown, N. / Debreczeni, J.E. / Ugochukwu, E. / Umeano, C. / Pike, A.C.W. / Papagrigoriou, E. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S.
History
DepositionApr 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Gigaxonin


Theoretical massNumber of molelcules
Total (without water)16,3461
Polymers16,3461
Non-polymers00
Water00
1
A: Gigaxonin

A: Gigaxonin


Theoretical massNumber of molelcules
Total (without water)32,6912
Polymers32,6912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
Unit cell
Length a, b, c (Å)75.664, 75.664, 167.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Detailsthe biological unit can be assembled if the following symmetry operator is applied to chain A -X +1/2, Y, -Z -1/4

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Components

#1: Protein Gigaxonin / Kelch-like protein 16


Mass: 16345.512 Da / Num. of mol.: 1 / Fragment: BTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAN, GAN1, KLHL16 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) with pRARE / References: UniProt: Q9H2C0

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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: 3.67 Å3/Da / Density % sol: 66.47 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M NaNO3, 0.1 M Na2SO4, 0.05 M Na/KPO4, 0.0285 M (NH4)2SO4, 30% PEG3350, 10% Ethylene glycol pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.4→44.9 Å / Num. all: 9876 / Num. obs: 9876 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.85 % / Rmerge(I) obs: 0.0756
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6906 / Num. unique all: 1102 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BUO

1buo


Resolution: 2.4→44.9 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.94 / SU B: 17.287 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.259 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29556 474 4.8 %RANDOM
Rwork0.28121 ---
all0.28185 9409 --
obs0.28185 9409 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 0 0 852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021863
X-RAY DIFFRACTIONr_bond_other_d0.0010.02546
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9751175
X-RAY DIFFRACTIONr_angle_other_deg0.90931334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.24622.41429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89515127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.798156
X-RAY DIFFRACTIONr_chiral_restr0.070.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02174
X-RAY DIFFRACTIONr_nbd_refined0.1910.2159
X-RAY DIFFRACTIONr_nbd_other0.1850.2519
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2410
X-RAY DIFFRACTIONr_nbtor_other0.0840.2473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5461.5603
X-RAY DIFFRACTIONr_mcbond_other0.1051.5234
X-RAY DIFFRACTIONr_mcangle_it0.8962932
X-RAY DIFFRACTIONr_scbond_it1.3833293
X-RAY DIFFRACTIONr_scangle_it2.1644.5243
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 35 -
Rwork0.257 675 -
obs--99.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.176-0.6301-0.3023.471-0.49555.5707-0.0631-0.96850.53950.75280.36570.0716-0.2361-0.0319-0.3027-0.1840.0419-0.0430.1-0.0044-0.023313.711533.8588-13.4263
221.05520.8103-0.132471.5455-57.569464.71981.3658-0.8038-2.72512.24620.90871.96664.1084-2.435-2.27450.3656-0.0044-0.03860.52060.11090.5375.449718.4856-6.4137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 11819 - 136
2X-RAY DIFFRACTION2AA119 - 125137 - 143

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