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- PDB-5oh1: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 5oh1
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Aminoglutethimide
ComponentsCereblon isoform 4
KeywordsUNKNOWN FUNCTION / Teratogenicity / Protein degradation / Substrate recognition / Ubiquitin ligase
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-9UQ / S-Thalidomide / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBoichenko, I. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / Hartmann, M.D.
CitationJournal: Acs Omega / Year: 2018
Title: Chemical Ligand Space of Cereblon.
Authors: Boichenko, I. / Bar, K. / Deiss, S. / Heim, C. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / Hartmann, M.D.
History
DepositionJul 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cereblon isoform 4
B: Cereblon isoform 4
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0569
Polymers41,1113
Non-polymers9456
Water2,828157
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0273
Polymers13,7041
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0273
Polymers13,7041
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0013
Polymers13,7041
Non-polymers2982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.831, 60.446, 88.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cereblon isoform 4


Mass: 13703.577 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EF2 / S-Thalidomide


Mass: 258.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#4: Chemical ChemComp-9UQ / (3~{R})-3-(4-aminophenyl)-3-ethyl-piperidine-2,6-dione


Mass: 232.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate PH 4.6, 15 %(W/V) PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→37.5 Å / Num. obs: 34222 / % possible obs: 99.7 % / Redundancy: 3.45 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 5404 / CC1/2: 0.76 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2Y

4v2y


Resolution: 1.7→37.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.723 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20972 1710 5 %RANDOM
Rwork0.16634 ---
obs0.16846 32512 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.745 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0 Å2
2--1.58 Å20 Å2
3----1.09 Å2
Refinement stepCycle: 1 / Resolution: 1.7→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 58 157 2646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192621
X-RAY DIFFRACTIONr_bond_other_d0.0010.022365
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9383558
X-RAY DIFFRACTIONr_angle_other_deg0.94935418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5355319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89821.707123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59815387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7891523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6867.4651249
X-RAY DIFFRACTIONr_mcbond_other2.6857.4651248
X-RAY DIFFRACTIONr_mcangle_it3.48812.4821559
X-RAY DIFFRACTIONr_mcangle_other3.48712.4831560
X-RAY DIFFRACTIONr_scbond_it4.4179.4281372
X-RAY DIFFRACTIONr_scbond_other4.4169.431373
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.19715.1351994
X-RAY DIFFRACTIONr_long_range_B_refined8.57638.5462994
X-RAY DIFFRACTIONr_long_range_B_other8.56138.2042966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 120 -
Rwork0.259 2328 -
obs--98.67 %
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)
12.24330.32940.98412.33761.2574.77480.06060.1562-0.2727-0.0358-0.0290.06350.1222-0.038-0.03160.01160.0163-0.01650.0475-0.04270.050719.366817.9911.9721
23.6524-1.26650.29562.7495-0.47062.77970.02120.0456-0.1720.0076-0.02990.1830.01550.07450.00870.0891-0.01890.00870.0067-0.00370.016232.04777.719124.0948
33.28491.90680.47764.7119-0.44363.257-0.0002-0.0083-0.0845-0.26520.07050.41380.366-0.4265-0.07030.1728-0.0468-0.00640.1432-0.00990.119628.1569-6.6861-6.618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 124
2X-RAY DIFFRACTION2B20 - 123
3X-RAY DIFFRACTION3C18 - 151

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