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- PDB-5oh8: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 5oh8
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Rolipram
ComponentsCereblon isoform 4
KeywordsUNKNOWN FUNCTION / Teratogenicity / Protein degradation / Substrate recognition / Ubiquitin ligase
Function / homologyCULT domain / CULT domain profile. / metal ion binding / ROLIPRAM / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)41,8588
Polymers41,1113
Non-polymers7475
Water1,47782
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0443
Polymers13,7041
Non-polymers3412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0443
Polymers13,7041
Non-polymers3412
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)57.339, 59.523, 88.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-ROL / ROLIPRAM / (4R)-[3-(CYCLOPENTYLOXY)-4-METHOXYPHENYL]-2-PYRROLIDINONE


Mass: 275.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant, inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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-F / Detector: PIXEL / Date: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→37.3 Å / Num. obs: 22598 / % possible obs: 99.8 % / Redundancy: 4.64 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 4.64 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 3569 / CC1/2: 0.78 / % possible all: 99.4

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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: 1.95→37.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.806 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22024 1135 5 %RANDOM
Rwork0.17824 ---
obs0.1803 21463 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2--1.81 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 1.95→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 43 82 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192079
X-RAY DIFFRACTIONr_bond_other_d0.0010.021923
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9482803
X-RAY DIFFRACTIONr_angle_other_deg0.9134403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29721.93593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0661518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
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_it2.2383.0441018
X-RAY DIFFRACTIONr_mcbond_other2.2393.0441017
X-RAY DIFFRACTIONr_mcangle_it3.164.5431263
X-RAY DIFFRACTIONr_mcangle_other3.1594.5431264
X-RAY DIFFRACTIONr_scbond_it3.2543.4421061
X-RAY DIFFRACTIONr_scbond_other3.2523.4421062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8235.0211539
X-RAY DIFFRACTIONr_long_range_B_refined7.18825.3992257
X-RAY DIFFRACTIONr_long_range_B_other7.19325.2562243
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 88 -
Rwork0.272 1534 -
obs--99.08 %
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)
13.30170.72171.14052.37631.49596.1074-0.03930.2337-0.2978-0.07920.04620.03560.0218-0.0122-0.00690.01050.0101-0.010.048-0.0450.049519.616917.65171.846
24.0099-2.1995-0.01235.2313-0.49172.863-0.0294-0.168-0.16220.2112-0.01560.06990.05430.10090.0450.0816-0.01740.00240.01620.00840.007332.27717.970524.1667
34.9611-1.56330.96596.87970.38555.4391-0.03760.054-0.67720.17-0.18270.92890.5379-0.75790.22040.306-0.13910.11850.3761-0.16530.401633.3821-1.0635-4.9619
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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