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

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Basic information

Entry
Database: PDB / ID: 7pjk
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / THALIDOMIDE ANALOGUES
Function / homologyCULT domain / CULT domain profile. / metal ion binding / (3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHeim, C. / Hartmann, M.D. / Maiwald, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J Enzyme Inhib Med Chem / Year: 2022
Title: Replacing the phthalimide core in thalidomide with benzotriazole.
Authors: Krasavin, M. / Bubyrev, A. / Kazantsev, A. / Heim, C. / Maiwald, S. / Zhukovsky, D. / Dar'in, D. / Hartmann, M.D. / Bunev, A.
History
DepositionAug 24, 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

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)41,7678
Polymers41,1113
Non-polymers6575
Water1,08160
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9993
Polymers13,7041
Non-polymers2962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9993
Polymers13,7041
Non-polymers2962
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)56.779, 59.435, 88.189
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 19 - 123 / Label seq-ID: 20 - 124

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 MSR-1 (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-7SE / (3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione


Mass: 230.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.81 Å3/Da / Density % sol: 32.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M (NH4)2HPO4

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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 EIGER2 X 16M / Detector: PIXEL / Date: May 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→35.44 Å / Num. obs: 21052 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.9
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 13 % / Rmerge(I) obs: 1.81 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 3305 / CC1/2: 0.583 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v2y

4v2y


Resolution: 1.99→35.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.789 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 1049 5 %RANDOM
Rwork0.2085 ---
obs0.2107 20002 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.06 Å2 / Biso mean: 51.966 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-0 Å20 Å2
2--1.64 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.99→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 37 60 2156
Biso mean--48.1 55.89 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132186
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171961
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.6362955
X-RAY DIFFRACTIONr_angle_other_deg1.1261.5764491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5655265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64620.088114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98415319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2051517
X-RAY DIFFRACTIONr_chiral_restr0.0460.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02588
Refine LS restraints NCS

Ens-ID: 1 / Number: 3065 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.99→2.041 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 70 -
Rwork0.313 1411 -
obs--96.11 %
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)
13.20280.58681.37952.45431.54155.57590.02290.1089-0.2982-0.05560.01620.12780.12020.0545-0.03910.04260.0187-0.02210.0175-0.02540.059419.27317.672.12
23.3996-1.82780.03124.468-0.72732.9766-0.013-0.0888-0.04730.09720.0152-0.1018-0.00580.189-0.00220.086-0.00880.00380.0155-0.00010.006232.0217.65123.891
32.94651.93941.50766.53161.78274.19170.0027-0.013-0.37610.2543-0.26680.94180.463-1.00060.26410.3225-0.1060.15330.4504-0.11810.492432.096-3.468-6.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 123
2X-RAY DIFFRACTION1A201 - 202
3X-RAY DIFFRACTION2B19 - 123
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C19 - 123
6X-RAY DIFFRACTION3C201

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