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- PDB-5oh2: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 5oh2
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pyrrolidin-2-one (Butyrolactam)
ComponentsCereblon isoform 4
KeywordsUNKNOWN FUNCTION / Teratogenicity / Protein degradation / Substrate recognition / Ubiquitin ligase
Function / homologyCULT domain / CULT domain profile. / metal ion binding / pyrrolidin-2-one / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)41,5629
Polymers41,1113
Non-polymers4526
Water2,450136
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8543
Polymers13,7041
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8543
Polymers13,7041
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8543
Polymers13,7041
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.911, 59.686, 88.443
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: _ / 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
11SERSERPROPROAA20 - 12221 - 123
21SERSERPROPROBB20 - 12221 - 123
12ALAALAALAALAAA19 - 12320 - 124
22ALAALAALAALACC19 - 12320 - 124
13SERSERALAALABB20 - 12321 - 124
23SERSERALAALACC20 - 12321 - 124

NCS ensembles :
ID
1
2
3

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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-BAQ / pyrrolidin-2-one


Mass: 85.104 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.4 Å / Num. obs: 24410 / % possible obs: 98.4 % / Redundancy: 2.86 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.81 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 3836 / CC1/2: 0.79 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V2Y

2v2y
PDB Unreleased entry


Resolution: 1.9→37.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.031 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22474 1218 5 %RANDOM
Rwork0.17654 ---
obs0.1789 23182 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.434 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0 Å2
2--1.2 Å20 Å2
3----1.52 Å2
Refinement stepCycle: 1 / Resolution: 1.9→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 21 136 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192554
X-RAY DIFFRACTIONr_bond_other_d0.0080.022309
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9173456
X-RAY DIFFRACTIONr_angle_other_deg1.41135288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95221.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9641521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212948
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02699
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_it1.4342.1731249
X-RAY DIFFRACTIONr_mcbond_other1.4352.1731247
X-RAY DIFFRACTIONr_mcangle_it2.2253.2481552
X-RAY DIFFRACTIONr_mcangle_other2.2243.2481553
X-RAY DIFFRACTIONr_scbond_it2.0822.4411305
X-RAY DIFFRACTIONr_scbond_other2.0812.4411306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2813.571902
X-RAY DIFFRACTIONr_long_range_B_refined6.11318.6652866
X-RAY DIFFRACTIONr_long_range_B_other6.06518.4492836
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)
11A53430.15
12B53430.15
21A48940.15
22C48940.15
31B48060.16
32C48060.16
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 80 -
Rwork0.274 1635 -
obs--96.02 %
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)
12.34720.31921.14052.23511.29155.00080.05440.1291-0.2776-0.0586-0.02090.06410.1969-0.0027-0.03350.01690.0117-0.01140.0494-0.04480.068719.265417.6762.0782
23.8824-1.89230.23033.2158-0.532.7351-0.0132-0.0208-0.1384-0.00660.00010.05910.04170.05280.01310.0536-0.01290.00530.00510.00040.00632.08087.319823.9021
34.10711.4941.045.3837-0.22684.7798-0.0282-0.1441-0.2783-0.20130.0480.7790.58-0.906-0.01970.2424-0.09410.02570.3438-0.02780.283728.2516-6.3726-7.0365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 151
2X-RAY DIFFRACTION2B20 - 151
3X-RAY DIFFRACTION3C18 - 151

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