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- PDB-4v2y: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 4v2y
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide
ComponentsCEREBLON ISOFORM 4
KeywordsSIGNALING PROTEIN / TERATOGENICITY / AROMATIC CAGE
Function / homologyPeptide methionine sulfoxide reductase. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / CULT domain / CULT domain profile. / Beta Complex / Mainly Beta / metal ion binding / S-Thalidomide / Cereblon isoform 4
Function and homology information
Biological speciesMAGNETOSPIRILLUM GRYPHISWALDENSE (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsHartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Thalidomide Mimics Uridine Binding to an Aromatic Cage in Cereblon.
Authors: Hartmann, M.D. / Boichenko, I. / Coles, M. / Zanini, F. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionOct 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)42,0829
Polymers41,1113
Non-polymers9716
Water3,873215
1
A: 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
MethodPISA
2
B: 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
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)56.490, 60.040, 88.470
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)
Strain: MSR-1 / 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-EF2 / S-Thalidomide


Mass: 258.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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 % / Description: NONE
Crystal growDetails: 0.1 M MAGNESIUM CHLORIDE, 0.1 M SODIUM CITRATE PH 5, 15%(W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→37.3 Å / Num. obs: 60181 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.69 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.46
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.39 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.73 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→37.33 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.929 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19457 3003 5 %RANDOM
Rwork0.16201 ---
obs0.16363 57028 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.4→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 60 215 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192666
X-RAY DIFFRACTIONr_bond_other_d0.0010.022398
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.9413638
X-RAY DIFFRACTIONr_angle_other_deg0.93335500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26621.901121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48615390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2511521
X-RAY DIFFRACTIONr_chiral_restr0.1340.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213094
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02725
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 213 -
Rwork0.319 4012 -
obs--96.4 %
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)
11.44570.13440.89881.25010.87933.44120.05850.0499-0.15020.0097-0.00430.05170.1377-0.0057-0.05430.00750.0085-0.00740.0653-0.02540.0719.282717.93082.133
21.8702-0.80530.3241.8085-0.42241.5334-0.0055-0.0069-0.14110.024-0.00060.11890.0267-0.02510.00610.0292-0.01170.01060.05260.0130.056631.73257.708924.0094
32.67971.39540.313.00980.03782.50630.02190.0127-0.1005-0.12720.01360.27550.1874-0.3183-0.03550.0869-0.01070.00870.1352-0.00610.120427.79-6.5007-6.895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 123
2X-RAY DIFFRACTION2B20 - 123
3X-RAY DIFFRACTION3C19 - 123

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