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- PDB-5oh4: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 5oh4
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidine-2,6-dione (Glutarimide)
ComponentsCereblon isoform 4
KeywordsUNKNOWN FUNCTION / Teratogenicity / Protein degradation / Substrate recognition / Ubiquitin ligase
Function / homologyCULT domain / CULT domain profile. / metal ion binding / piperidine-2,6-dione / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)41,6469
Polymers41,1113
Non-polymers5366
Water1,24369
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8823
Polymers13,7041
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8823
Polymers13,7041
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8823
Polymers13,7041
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.180, 59.661, 88.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROAA20 - 12221 - 123
21SERSERPROPROBB20 - 12221 - 123
12ALAALAALAALAAA19 - 12320 - 124
22ALAALAALAALACC19 - 12320 - 124
13SERSERALAALABB20 - 12321 - 124
23SERSERALAALACC20 - 12321 - 124

NCS ensembles :
ID
1
2
3

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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-9UZ / piperidine-2,6-dione


Mass: 113.115 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.3→37.1 Å / Num. obs: 13628 / % possible obs: 97 % / Redundancy: 2.55 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.64
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 2102 / CC1/2: 0.86 / % possible all: 94

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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: 2.3→37.1 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.904 / SU B: 16.663 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.259 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25008 678 5 %RANDOM
Rwork0.18929 ---
obs0.19228 12940 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.714 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0 Å2
2--3.54 Å2-0 Å2
3----2.82 Å2
Refinement stepCycle: 1 / Resolution: 2.3→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 27 69 2511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192526
X-RAY DIFFRACTIONr_bond_other_d0.0070.022278
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9193416
X-RAY DIFFRACTIONr_angle_other_deg1.31535210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26821.78118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12515365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8061521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212918
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02689
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_it1.2952.2961234
X-RAY DIFFRACTIONr_mcbond_other1.2962.2951233
X-RAY DIFFRACTIONr_mcangle_it2.0193.4371536
X-RAY DIFFRACTIONr_mcangle_other2.0183.4381537
X-RAY DIFFRACTIONr_scbond_it1.7362.4961292
X-RAY DIFFRACTIONr_scbond_other1.7362.4971291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7883.6671880
X-RAY DIFFRACTIONr_long_range_B_refined4.75118.9542771
X-RAY DIFFRACTIONr_long_range_B_other4.7418.9152762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A54350.13
12B54350.13
21A48090.15
22C48090.15
31B46520.16
32C46520.16
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 45 -
Rwork0.29 879 -
obs--91.76 %
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)
12.90550.29560.8782.99171.17554.65860.05520.0818-0.3255-0.1253-0.02370.11630.28820.0204-0.03150.13060.0341-0.01760.047-0.03770.062618.902117.61232.1684
24.1099-1.4320.54573.5072-0.28642.7061-0.0539-0.0124-0.17820.00450.05110.10.01280.08240.00280.1402-0.01030.0140.00640.00290.01131.75667.456523.9362
34.3092.66150.85543.9911-0.63952.079-0.0032-0.1169-0.0274-0.18670.11740.3440.0514-0.4588-0.11420.33950.00220.02130.28220.01110.191727.7706-6.5428-6.8891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 151
2X-RAY DIFFRACTION2B20 - 151
3X-RAY DIFFRACTION3C18 - 151

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