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- PDB-2woz: The novel beta-propeller of the BTB-Kelch protein Krp1 provides t... -

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Basic information

Entry
Database: PDB / ID: 2woz
TitleThe novel beta-propeller of the BTB-Kelch protein Krp1 provides the binding site for Lasp-1 that is necessary for pseudopodia extension
ComponentsKELCH REPEAT AND BTB DOMAIN-CONTAINING PROTEIN 10
KeywordsPROTEIN BINDING / INVASION AND METASTASIS / UBL CONJUGATION PATHWAY / UBL PROTEIN FOLDING / CELL PROJECTION / CYTOSKELETON / KELCH REPEAT / KELCH DOMAIN
Function / homology
Function and homology information


regulation of myoblast proliferation / pseudopodium assembly / regulation of skeletal muscle cell differentiation / regulation of myoblast differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / myofibril assembly / M band / Cul3-RING ubiquitin ligase complex / skeletal muscle cell differentiation ...regulation of myoblast proliferation / pseudopodium assembly / regulation of skeletal muscle cell differentiation / regulation of myoblast differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / myofibril assembly / M band / Cul3-RING ubiquitin ligase complex / skeletal muscle cell differentiation / pseudopodium / ruffle / sarcoplasmic reticulum membrane / cytoskeleton / protein ubiquitination / endoplasmic reticulum membrane / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kelch-like protein 41 / Kelch-type beta propeller / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller ...Kelch-like protein 41 / Kelch-type beta propeller / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / 6 Propeller / Neuraminidase / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Kelch-like protein 41
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGray, C.H. / McGarry, L.C. / Spence, H.J. / Riboldi-Tunnicliffe, A. / Ozanne, B.W.
CitationJournal: J. Biol. Chem. / Year: 2009
Title: Novel beta-propeller of the BTB-Kelch protein Krp1 provides a binding site for Lasp-1 that is necessary for pseudopodial extension.
Authors: Gray, C.H. / McGarry, L.C. / Spence, H.J. / Riboldi-Tunnicliffe, A. / Ozanne, B.W.
History
DepositionJul 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / diffrn_radiation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KELCH REPEAT AND BTB DOMAIN-CONTAINING PROTEIN 10


Theoretical massNumber of molelcules
Total (without water)35,4181
Polymers35,4181
Non-polymers00
Water3,009167
1
A: KELCH REPEAT AND BTB DOMAIN-CONTAINING PROTEIN 10

A: KELCH REPEAT AND BTB DOMAIN-CONTAINING PROTEIN 10


Theoretical massNumber of molelcules
Total (without water)70,8372
Polymers70,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3570 Å2
ΔGint-17.2 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.110, 98.530, 46.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein KELCH REPEAT AND BTB DOMAIN-CONTAINING PROTEIN 10 / KRP1 / KELCH-RELATED PROTEIN 1 / KEL-LIKE PROTEIN 23 / SARCOSIN


Mass: 35418.426 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN, RESIDUES 289-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9ER30
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42 % / Description: NONE

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→45.9 Å / Num. obs: 20693 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 30.235 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→49.5 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 -5 %RANDOM
Rwork0.237 ---
obs-20693 97.1 %-
Refinement stepCycle: LAST / Resolution: 2→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 0 167 2556
LS refinement shellResolution: 2→2.11 Å / Num. reflection Rwork: 3049

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