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- PDB-3i3n: Crystal structure of the BTB-BACK domains of human KLHL11 -

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Basic information

Entry
Database: PDB / ID: 3i3n
TitleCrystal structure of the BTB-BACK domains of human KLHL11
ComponentsKelch-like protein 11
KeywordsPROTEIN BINDING / Structural Genomics / BTB / KLHL11A / SGC / Structural Genomics Consortium / Kelch repeat / Secreted
Function / homology
Function and homology information


Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Kelch-like protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMurray, J.W. / Cooper, C.D.O. / Krojer, T. / Mahajan, P. / Salah, E. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Roos, A. / Muniz, J. ...Murray, J.W. / Cooper, C.D.O. / Krojer, T. / Mahajan, P. / Salah, E. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Roos, A. / Muniz, J. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the BTB-BACK domains of human KLHL11
Authors: Murray, J.W. / Cooper, C.D.O. / Krojer, T. / Mahajan, P. / Salah, E. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Roos, A. / Muniz, J. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / ...Authors: Murray, J.W. / Cooper, C.D.O. / Krojer, T. / Mahajan, P. / Salah, E. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Roos, A. / Muniz, J. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC)
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Kelch-like protein 11
B: Kelch-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7136
Polymers65,5492
Non-polymers1644
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-51 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.093, 68.879, 136.834
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kelch-like protein 11


Mass: 32774.398 Da / Num. of mol.: 2 / Fragment: BTB-BACK domains (UNP residues 67-340)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL11, KLHL11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVR0
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.25M K thiocyanate, 25w/v PEG 3350, 5v/v ethylene glycol, bis tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9959 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9959 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 23589 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 64.8 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3369 / Rsym value: 0.492 / % possible all: 98.2

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→26.33 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1206 -RANDOM
Rwork0.26 ---
all-23505 --
obs-23387 99.5 %-
Displacement parametersBiso mean: 69.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 6 80 4450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007953
X-RAY DIFFRACTIONc_angle_deg1.24981
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.041
RfactorNum. reflection% reflection
Rfree0.393 93 -
Rwork0.36 --
obs-2165 97 %

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