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- PDB-6r0s: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r0s
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and hydrolysis product
Components
  • CEREBLON ISOFORM 4
  • Cereblon isoform 4
KeywordsSIGNALING PROTEIN / ----
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Chem-JOE / Chem-JOH / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 13, 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 / refine / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _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)42,66013
Polymers41,3844
Non-polymers1,2769
Water4,017223
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
F: CEREBLON ISOFORM 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4806
Polymers13,9772
Non-polymers5034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0583
Polymers13,7041
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.455, 58.824, 88.234
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: _ / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA19 - 12220 - 123
21ALAALABB19 - 12220 - 123
12PROPROAA17 - 12218 - 123
22PROPROCC17 - 12218 - 123
13ALAALABB19 - 12220 - 123
23ALAALACC19 - 12220 - 123

NCS ensembles :
ID
1
2
3

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Components

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Protein / Protein/peptide , 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: 273.330 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 , 7 types, 232 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


Mass: 258.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 307.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9N3O7
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-JOH / 2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione


Mass: 289.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H7N3O6
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.77 Å3/Da / Density % sol: 30.58 %
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: 1.55→44.12 Å / Num. obs: 43510 / % possible obs: 99.8 % / Redundancy: 12.66 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.09
Reflection shellResolution: 1.55→1.64 Å / Rmerge(I) obs: 0.98 / Num. unique obs: 6861 / CC1/2: 0.85 / % possible all: 98.9

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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: 1.55→44.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.045 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21293 2173 5 %RANDOM
Rwork0.18685 ---
obs0.18815 41337 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.054 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0 Å2
2--0.99 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.55→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 76 223 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192754
X-RAY DIFFRACTIONr_bond_other_d0.0020.022398
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9363746
X-RAY DIFFRACTIONr_angle_other_deg1.0173.0015529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47221.967122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96315393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0441521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213136
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02666
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_it1.1322.1331319
X-RAY DIFFRACTIONr_mcbond_other1.1312.1311318
X-RAY DIFFRACTIONr_mcangle_it1.9253.1831648
X-RAY DIFFRACTIONr_mcangle_other1.9243.1851649
X-RAY DIFFRACTIONr_scbond_it1.3642.2881435
X-RAY DIFFRACTIONr_scbond_other1.3642.2891436
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2313.3882090
X-RAY DIFFRACTIONr_long_range_B_refined4.50724.6373126
X-RAY DIFFRACTIONr_long_range_B_other4.50724.6513127
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)
11A65300.11
12B65300.11
21A61200.14
22C61200.14
31B59460.15
32C59460.15
LS refinement shellResolution: 1.547→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 146 -
Rwork0.283 2950 -
obs--97.51 %
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)
10.8666-0.05640.61550.08760.08811.21990.0314-0.0367-0.0317-0.01420.01550.03790.00460.0168-0.04690.0070.0038-0.00940.0687-0.01980.035818.922217.38842.4936
20.8321-0.4925-0.16450.525-0.32030.920.0285-0.0536-0.0655-0.0289-0.02110.0476-0.04030.0561-0.00740.032-0.00170.00030.05690.01080.026831.7527.455423.7948
31.58780.77461.27931.27640.17361.25950.0661-0.2165-0.12230.06550.0678-0.00060.0315-0.2581-0.13390.0146-0.00370.00840.12840.03220.025827.517-6.2614-6.9819
400000000000000-00.0218000.021800.0218000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 395
2X-RAY DIFFRACTION2B19 - 389
3X-RAY DIFFRACTION3C17 - 339

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