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- PDB-7qzq: Crystal structure of the kelch domain of human KBTBD12 -

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Basic information

Entry
Database: PDB / ID: 7qzq
TitleCrystal structure of the kelch domain of human KBTBD12
ComponentsKelch repeat and BTB domain-containing protein 12
KeywordsLIGASE / E3 ligase / Kelch / BTB-Kelch
Function / homology
Function and homology information


BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. ...BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / 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
Similarity search - Domain/homology
Kelch repeat and BTB domain-containing protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsManning, C.E. / Chen, Z. / Chen, X. / Bradshaw, W.J. / Bakshi, S. / Mckinley, G. / Chalk, R. / Burgess-Brown, N. / von Delft, F. / Bullock, A.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the kelch domain of human KBTBD12
Authors: Manning, C.E. / Chen, Z. / Chen, X. / Bakshi, S. / Mckinley, G. / Chalk, R. / Burgess-Brown, N. / von Delft, F. / Bullock, A.N.
History
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / pdbx_initial_refinement_model
Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch repeat and BTB domain-containing protein 12
B: Kelch repeat and BTB domain-containing protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8114
Polymers81,7262
Non-polymers852
Water8,035446
1
A: Kelch repeat and BTB domain-containing protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9252
Polymers40,8631
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch repeat and BTB domain-containing protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8862
Polymers40,8631
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.379, 55.078, 95.164
Angle α, β, γ (deg.)90.000, 108.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kelch repeat and BTB domain-containing protein 12 / Kelch domain-containing protein 6


Mass: 40863.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KBTBD12, KLHDC6 / Cell line (production host): Sf9
Production host: Spodoptera frugiperda multiple nucleopolyhedrovirus
References: UniProt: Q3ZCT8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 8% PEG4000 -- 0.1M acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.88→65.63 Å / Num. obs: 57704 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 32.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.17 / Net I/σ(I): 7.3
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 5.6 % / Rmerge(I) obs: 3.1 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2827 / CC1/2: 0.268 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.88 Å65.63 Å
Translation1.88 Å65.63 Å

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Processing

Software
NameVersionClassification
XDSFeb 5, 2021 (BUILT 20210323)data reduction
Aimless0.7.7data scaling
PHASER2.8.1phasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPJ

2vpj


Resolution: 1.88→45.08 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 2868 5.06 %
Rwork0.1947 53847 -
obs0.1971 56715 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.14 Å2 / Biso mean: 40.4986 Å2 / Biso min: 22.73 Å2
Refinement stepCycle: final / Resolution: 1.88→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 5 446 5733
Biso mean--41.3 43.94 -
Num. residues----685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.920.37961150.38822085220077
1.92-1.950.39631100.35542545265591
1.95-1.990.38241280.33732667279598
1.99-2.030.34881500.30532727287799
2.03-2.070.34411350.289327352870100
2.07-2.120.34081350.273727102845100
2.12-2.170.30651500.247926902840100
2.17-2.230.29191490.243427142863100
2.23-2.30.29381330.214727162849100
2.3-2.370.26081600.208427202880100
2.37-2.460.29991460.212727232869100
2.46-2.560.27671380.205927542892100
2.56-2.670.2531400.199227262866100
2.67-2.810.22441380.184527512889100
2.81-2.990.26951500.190927432893100
2.99-3.220.24081210.187627772898100
3.22-3.550.22721390.175627492888100
3.55-4.060.21841780.165427392917100
4.06-5.110.18941780.142427462924100
5.11-45.080.19971750.179228303005100

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