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- PDB-6r19: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r19
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a
Components(Cereblon isoform ...) x 2
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Chem-JON / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHeim, C. / Hartmann, M.D.
CitationJournal: J.Med.Chem. / Year: 2019
Title: De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives.
Authors: Heim, C. / Pliatsika, D. / Mousavizadeh, F. / Bar, K. / Hernandez Alvarez, B. / Giannis, A. / Hartmann, M.D.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
F: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,87813
Polymers41,6394
Non-polymers1,2399
Water5,062281
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1224
Polymers13,7041
Non-polymers4193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2005
Polymers13,7041
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
4
F: Cereblon isoform 4


  • defined by author
  • 529 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5291
Polymers5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.557, 59.234, 88.425
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: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA19 - 12220 - 123
21BB19 - 12220 - 123
12AA16 - 12217 - 123
22CC16 - 12217 - 123
13BB19 - 12220 - 123
23CC19 - 12220 - 123

NCS ensembles :
ID
1
2
3

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Components

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Cereblon isoform ... , 2 types, 4 molecules ABCF

#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 MSR-1 (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0
#2: Protein/peptide Cereblon isoform 4


Mass: 528.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 290 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 258.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-JON / [(2~{S})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate


Mass: 241.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 1.78 Å3/Da / Density % sol: 30.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.4 M Ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→49.26 Å / Num. obs: 53406 / % possible obs: 99.8 % / Redundancy: 12.75 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.83
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 8403 / CC1/2: 0.86 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2Y

4v2y


Resolution: 1.45→49.26 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.59 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20068 2673 5 %RANDOM
Rwork0.17172 ---
obs0.17316 50733 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å2-0 Å2
2--1.2 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.45→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 73 282 2919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192790
X-RAY DIFFRACTIONr_bond_other_d0.0020.022445
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.9333797
X-RAY DIFFRACTIONr_angle_other_deg1.0662.9915650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79721.641128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4615401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6991524
X-RAY DIFFRACTIONr_chiral_restr0.1190.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213175
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02685
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_it1.4561.6741342
X-RAY DIFFRACTIONr_mcbond_other1.4411.6711341
X-RAY DIFFRACTIONr_mcangle_it2.3252.4971676
X-RAY DIFFRACTIONr_mcangle_other2.3272.4991677
X-RAY DIFFRACTIONr_scbond_it2.0761.9031448
X-RAY DIFFRACTIONr_scbond_other2.0751.9051449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1782.7792111
X-RAY DIFFRACTIONr_long_range_B_refined6.10120.2563205
X-RAY DIFFRACTIONr_long_range_B_other6.120.2673206
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)
11A63180.13
12B63180.13
21A59740.16
22C59740.16
31B58280.17
32C58280.17
LS refinement shellResolution: 1.449→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 191 -
Rwork0.313 3583 -
obs--96.55 %
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)
11.1257-0.04870.66850.50660.05951.79660.0592-0.0383-0.04680.00930.01090.04170.0478-0.0173-0.07010.0220.002-0.00630.0191-0.01460.022918.796517.24933.0783
21.362-0.712-0.22620.9448-0.19171.10860.0133-0.0522-0.0534-0.0291-0.02720.0357-0.02430.05030.01390.0479-0.01010.00390.0120.0060.020331.87837.515323.8023
31.47130.45470.56511.39980.0611.24530.0396-0.1666-0.07110.03330.03050.07040.0802-0.2022-0.070.0212-0.01550.00350.04190.0170.013827.4066-5.9432-7.2043
41.756-0.78340.76654.31276.147911.0864-0.01590.03660.3181-0.1755-0.0249-0.17-0.3673-0.08320.04080.05470.02530.03230.07580.03380.083944.9061-11.729112.516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 160
2X-RAY DIFFRACTION2B19 - 161
3X-RAY DIFFRACTION3C16 - 151
4X-RAY DIFFRACTION4F1 - 6

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