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- PDB-2vkp: Crystal structure of BTB domain from BTBD6 -

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Basic information

Entry
Database: PDB / ID: 2vkp
TitleCrystal structure of BTB domain from BTBD6
ComponentsBTB/POZ DOMAIN-CONTAINING PROTEIN 6
KeywordsPROTEIN BINDING / PROTEIN-BINDING
Function / homology
Function and homology information


neurogenesis / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cytosol
Similarity search - Function
: / PHR / PHR domain superfamily / PHR domain / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain ...: / PHR / PHR domain superfamily / PHR domain / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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
: / BTB/POZ domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCooper, C.D.O. / Pike, A.C.W. / Salah, E. / Filippakopoulos, P. / Bunkoczi, G. / Elkins, J.M. / von Delft, F. / Gileadi, O. / Edwards, A. / Weigelt, J. ...Cooper, C.D.O. / Pike, A.C.W. / Salah, E. / Filippakopoulos, P. / Bunkoczi, G. / Elkins, J.M. / von Delft, F. / Gileadi, O. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of Btb Domain from Btbd6
Authors: Cooper, C.D.O. / Pike, A.C.W. / Salah, E. / Filippakopoulos, P. / Bunkoczi, G. / Elkins, J.M. / von Delft, F. / Gileadi, O. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Knapp, S.
History
DepositionDec 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Revision 1.3Dec 13, 2017Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.gene_src_common_name ..._citation_author.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BTB/POZ DOMAIN-CONTAINING PROTEIN 6
B: BTB/POZ DOMAIN-CONTAINING PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4224
Polymers24,3212
Non-polymers1012
Water3,135174
1
A: BTB/POZ DOMAIN-CONTAINING PROTEIN 6
B: BTB/POZ DOMAIN-CONTAINING PROTEIN 6
hetero molecules

A: BTB/POZ DOMAIN-CONTAINING PROTEIN 6
B: BTB/POZ DOMAIN-CONTAINING PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8448
Polymers48,6424
Non-polymers2024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2920 Å2
ΔGint-46.5 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.135, 58.135, 332.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.874, -0.486, 0.027), (-0.486, 0.873, -0.023), (-0.012, -0.033, -0.999)
Vector: 77.49804, 20.90195, 41.86135)

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Components

#1: Protein BTB/POZ DOMAIN-CONTAINING PROTEIN 6 / LENS BTB DOMAIN PROTEIN / BTB DOMAIN PROTEIN BTBD6


Mass: 12160.424 Da / Num. of mol.: 2 / Fragment: BTB DOMAIN, RESIDUES 2-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-PRARE2 / References: UniProt: Q96KE9
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
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: 3.38 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 6.5
Details: 0.8M POTASSIUM CITRATE, 0.1M SODIUM CACODYLATE PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98248, 0.97874
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.982481
20.978741
ReflectionResolution: 1.9→50 Å / Num. obs: 27754 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 27.91 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→43.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.7 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1403 5.1 %RANDOM
Rwork0.194 ---
obs0.196 26222 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20.8 Å20 Å2
2--1.6 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 5 174 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221673
X-RAY DIFFRACTIONr_bond_other_d0.0010.021060
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9752284
X-RAY DIFFRACTIONr_angle_other_deg0.88932610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.225209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.40524.09861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72715254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.891152
X-RAY DIFFRACTIONr_chiral_restr0.0790.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined0.2140.2354
X-RAY DIFFRACTIONr_nbd_other0.2370.2923
X-RAY DIFFRACTIONr_nbtor_refined0.190.2869
X-RAY DIFFRACTIONr_nbtor_other0.1160.2718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.66231066
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.79651725
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.8778607
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.73211559
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 83
Rwork0.252 1907
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)
11.48820.1963-0.74161.57280.16762.5896-0.14690.1373-0.2094-0.1850.0727-0.06580.2356-0.03390.07420.2153-0.04410.06780.0307-0.0430.051141.284627.30090.6468
23.751-1.52180.71734.04830.27384.2659-0.08790.1362-0.3559-0.0115-0.089-0.09030.4830.20380.17690.215-0.05040.06270.018-0.02460.100738.04725.66667.3345
312.1811-8.3971-8.247915.74338.056716.31440.11140.29640.4379-0.5013-0.06190.3238-0.9255-0.5533-0.04950.2035-0.0319-0.00280.14380.01840.097534.034837.5386-0.1561
44.1874-0.2381-1.88132.74771.42944.9692-0.04720.07230.0682-0.170.00940.09520.0042-0.18480.03780.1602-0.03930.00990.0373-0.00330.086533.462535.955112.0509
514.1767-3.04680.85676.78712.106111.75280.0255-0.15840.38350.17450.02150.6156-0.4019-0.6739-0.0470.16010.01-0.00660.0952-0.01090.136625.14842.372617.7359
61.07740.38490.53291.7635-0.35254.4062-0.1454-0.1632-0.0365-0.28940.1158-0.26940.473-0.12090.02950.1619-0.14450.05470.1048-0.03150.047131.227424.415340.7777
75.1576-1.12120.77374.29-2.29361.7547-0.0807-0.2231-0.215-0.53590.19550.15060.4264-0.4137-0.11480.1723-0.2201-0.01640.1910.00910.011918.144721.985236.981
81.39230.3312-1.18115.251-0.51443.4641-0.14430.0141-0.0853-0.325-0.0219-0.10030.3859-0.27750.16620.1672-0.12370.03510.0886-0.03040.044132.301226.889433.1384
93.65436.8515-5.486717.1829-10.695913.46910.1359-0.20310.4060.3824-0.10950.3106-0.6832-0.119-0.02640.1043-0.0093-0.00220.1592-0.04040.130930.233237.627640.2326
101.79831.1036-0.09382.9251-0.9622.8259-0.1252-0.05060.064-0.0703-0.0054-0.08160.1349-0.2810.13060.1047-0.0888-0.00180.0867-0.03060.075732.090337.814426.6047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 42
2X-RAY DIFFRACTION2A49 - 67
3X-RAY DIFFRACTION3A68 - 73
4X-RAY DIFFRACTION4A74 - 100
5X-RAY DIFFRACTION5A101 - 108
6X-RAY DIFFRACTION6B0 - 33
7X-RAY DIFFRACTION7B34 - 50
8X-RAY DIFFRACTION8B51 - 68
9X-RAY DIFFRACTION9B69 - 74
10X-RAY DIFFRACTION10B75 - 108

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