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- PDB-4v32: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 4v32
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Y101F mutant
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 / SAD / Resolution: 1.9 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)42,0349
Polymers41,0633
Non-polymers9716
Water2,576143
1
A: CEREBLON ISOFORM 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0113
Polymers13,6881
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)14,0113
Polymers13,6881
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)14,0113
Polymers13,6881
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.753, 59.959, 88.414
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: 13687.577 Da / Num. of mol.: 3 / Mutation: YES
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.: 143 / 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: 0.2 M SODIUM CHLORIDE, 0.1 M PHOSPHATE-CITRATE PH 4.2, 20 %(W/V) PEG 8000

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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: Aug 3, 2012
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: 24442 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.99 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.06
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 6.91 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.59 / % possible all: 99.5

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Processing

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

Resolution: 1.9→37.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.03 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23987 1219 5 %RANDOM
Rwork0.18212 ---
obs0.18497 23212 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.613 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2--5.03 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 60 143 2597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192570
X-RAY DIFFRACTIONr_bond_other_d0.0010.022284
X-RAY DIFFRACTIONr_angle_refined_deg2.1611.9343490
X-RAY DIFFRACTIONr_angle_other_deg0.91335219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96221.897116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33215361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4831519
X-RAY DIFFRACTIONr_chiral_restr0.1240.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 86 -
Rwork0.241 1694 -
obs--99.39 %
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)
12.27570.2691.36361.61391.15334.51490.03110.1522-0.23620.0066-0.00780.06220.12480.0299-0.02330.17640.01110.00470.0716-0.03680.308219.37117.7952.0892
23.3302-1.38210.3512.6221-0.64432.5286-0.0035-0.0145-0.16680.0689-0.00490.09420.02470.04230.00840.2683-0.00730.01480.00160.0130.281431.92067.564323.9067
32.80931.33320.292.7174-0.79211.76740.0506-0.0226-0.19-0.17460.03340.34420.2963-0.4815-0.08410.4372-0.05740.02220.2868-0.03130.471328.4998-6.6455-6.8384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 123
2X-RAY DIFFRACTION2B20 - 123
3X-RAY DIFFRACTION3C18 - 123

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