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

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Basic information

Entry
Database: PDB / ID: 5ami
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash I structure
ComponentsCEREBLON ISOFORM 4
KeywordsSIGNALING PROTEIN / TERATOGENICITY / AROMATIC CAGE
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Cereblon isoform 4
Function and homology information
Biological speciesMAGNETOSPIRILLUM GRYPHISWALDENSE (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B.
CitationJournal: Plos One / Year: 2015
Title: Structural Dynamics of the Cereblon Ligand Binding Domain.
Authors: Hartmann, M.D. / Boichenko, I. / Coles, M. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionMar 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)41,8238
Polymers41,1113
Non-polymers7135
Water1,78399
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)13,7692
Polymers13,7041
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.250, 59.656, 86.728
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.: 2 / Source method: obtained synthetically / Formula: C13H10N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 100 MM SODIUM ACETATE PH 4.6, 20 %(W/V) PEG 6000

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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: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→37.3 Å / Num. obs: 30628 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.23 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.98
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 4.23 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V2Y

4v2y


Resolution: 1.75→37.29 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.736 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20942 1540 5 %RANDOM
Rwork0.16508 ---
obs0.16727 29087 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.758 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--0.03 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 41 99 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192357
X-RAY DIFFRACTIONr_bond_other_d0.0010.022136
X-RAY DIFFRACTIONr_angle_refined_deg2.2351.9353195
X-RAY DIFFRACTIONr_angle_other_deg1.15534882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26822.019104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4051517
X-RAY DIFFRACTIONr_chiral_restr0.1230.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it1.6651.6651154
X-RAY DIFFRACTIONr_mcbond_other1.6641.6651153
X-RAY DIFFRACTIONr_mcangle_it2.5662.4831433
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5251.9481203
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: 1.749→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 116 -
Rwork0.268 2083 -
obs--97.95 %
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)
12.60090.2670.42421.85191.09594.5139-0.05530.0939-0.2021-0.00480.04910.0373-0.0363-0.03010.00610.00540.0095-0.01120.1088-0.02550.084519.710817.65891.6802
22.4614-1.85370.10844.046-0.90252.0624-0.0146-0.0619-0.13290.2033-0.01920.03490.05170.04850.03380.0992-0.01840.00210.07550.01480.068432.25578.230923.7781
33.2703-0.28890.54454.9318-0.75683.5230.0127-0.0752-0.5061-0.19950.01320.59740.5577-0.5569-0.02590.3274-0.0940.05850.3265-0.03850.338130.6942-4.6346-4.1684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 151
2X-RAY DIFFRACTION2B20 - 151
3X-RAY DIFFRACTION3C16 - 150

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