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- PDB-7ps9: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 7ps9
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Iberdomide (CC-220)
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / PROTEIN DEGRADATION / Immunomodulatory imide drug / E3 LIGASE
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-8W7 / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHeim, C. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system.
Authors: Heim, C. / Hartmann, M.D.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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)42,4429
Polymers40,8983
Non-polymers1,5456
Water2,504139
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1473
Polymers13,6331
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1473
Polymers13,6331
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1473
Polymers13,6331
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.001, 58.850, 88.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
11ALAALAPROPROAA19 - 12219 - 122
21ALAALAPROPROBB19 - 12219 - 122
12GLYGLYALAALAAA18 - 12318 - 123
22GLYGLYALAALACC18 - 12318 - 123
13ALAALAALAALABB19 - 12319 - 123
23ALAALAALAALACC19 - 12319 - 123

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cereblon isoform 4


Mass: 13632.500 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 BL21(DE3) (bacteria) / 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-8W7 / (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione


Mass: 449.499 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H27N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.78 Å3/Da / Density % sol: 31.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M (NH4)H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.8→34.76 Å / Num. obs: 27318 / % possible obs: 97.7 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.141 / Net I/σ(I): 11.24
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 11 % / Rmerge(I) obs: 1.542 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 4220 / CC1/2: 0.845 / Rrim(I) all: 1.611 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v2y

4v2y


Resolution: 1.8→34.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.021 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1373 5 %RANDOM
Rwork0.1929 ---
obs0.1956 25945 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.23 Å2 / Biso mean: 37.589 Å2 / Biso min: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.09 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.8→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 102 139 2588
Biso mean--62.26 43.27 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122566
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172258
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6343482
X-RAY DIFFRACTIONr_angle_other_deg1.3351.5735182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.585305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58520.229131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21215343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3991517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A30610.11
12B30610.11
21A24630.12
22C24630.12
31B24080.14
32C24080.14
LS refinement shellResolution: 1.8→1.844 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.367 93 -
Rwork0.351 1777 -
obs--92.35 %

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