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- PDB-5oh3: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 5oh3
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Ethosuximide
ComponentsCereblon isoform 4
KeywordsUNKNOWN FUNCTION / Teratogenicity / Protein degradation / Substrate recognition / Ubiquitin ligase
Function / homologyCULT domain / CULT domain profile. / metal ion binding / (3~{S})-3-ethyl-3-methyl-pyrrolidine-2,5-dione / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)41,5898
Polymers41,1113
Non-polymers4795
Water2,072115
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9103
Polymers13,7041
Non-polymers2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9103
Polymers13,7041
Non-polymers2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7692
Polymers13,7041
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.880, 59.790, 88.100
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 20 - 122 / Label seq-ID: 21 - 123

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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-9V2 / (3~{S})-3-ethyl-3-methyl-pyrrolidine-2,5-dione


Mass: 141.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.1→37.4 Å / Num. obs: 18109 / % possible obs: 99.2 % / Redundancy: 3.39 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 2816 / % possible all: 97.1

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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: 2.1→37.33 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.44 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23066 901 5 %RANDOM
Rwork0.17947 ---
obs0.18199 17207 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å20 Å2
2--1.28 Å20 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.1→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 23 115 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192250
X-RAY DIFFRACTIONr_bond_other_d0.0040.022063
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9233041
X-RAY DIFFRACTIONr_angle_other_deg1.02334710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9255272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58521.827104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2141519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212571
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02608
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_it1.2062.3141100
X-RAY DIFFRACTIONr_mcbond_other1.2052.3141099
X-RAY DIFFRACTIONr_mcangle_it1.9423.4591365
X-RAY DIFFRACTIONr_mcangle_other1.9413.4591366
X-RAY DIFFRACTIONr_scbond_it1.5732.5121150
X-RAY DIFFRACTIONr_scbond_other1.5722.5121151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5313.6961676
X-RAY DIFFRACTIONr_long_range_B_refined6.09219.5612514
X-RAY DIFFRACTIONr_long_range_B_other5.98319.2342481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5371 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 61 -
Rwork0.225 1205 -
obs--98.14 %
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)
13.25090.88761.32792.22061.19224.89650.03240.1459-0.2939-0.02990.03410.08610.0760.0165-0.06650.00580.0151-0.01080.0707-0.03270.046419.325717.70042.0101
23.8053-1.82720.26823.9415-1.07532.845-0.0415-0.0294-0.26050.1397-0.00820.13470.020.05740.04970.0812-0.01130.01690.02470.00970.02531.99877.614123.9323
34.04941.2441.43426.01631.63184.3999-0.01050.1159-0.41490.0585-0.35961.06250.656-0.94730.37020.3613-0.13070.13180.4548-0.20620.391431.2626-3.185-7.3417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 151
2X-RAY DIFFRACTION2B20 - 151
3X-RAY DIFFRACTION3C18 - 150

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