PDB-5amk: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multi...

ID or keywords:

Entry

Database: PDB / ID: 5amk

Title

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form

Components

CEREBLON ISOFORM 4

Keywords

SIGNALING PROTEIN / TERATOGENICITY / AROMATIC CAGE

Function / homology

Peptide 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 species

MAGNETOSPIRILLUM GRYPHISWALDENSE (magnetotactic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Hartmann, M.D. / Lupas, A.N. / Hernandez Alvarez, B.

Citation

Journal: 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

Deposition	Mar 10, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5amk.cif.gz	184.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5amk.ent.gz	149.9 KB	Display	PDB format
PDBx/mmJSON format	5amk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/5amk ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amk	HTTPS FTP

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Related structure data

Related structure data	5amhC 5amiC 5amjC 4v2yS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4v2y-1 4v2y-2 4v2z-2 2m5w-d 4qsy-d 1kaf-6 5ami-1 5oh8-2 2r2z-d 6r12-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CEREBLON ISOFORM 4

B: CEREBLON ISOFORM 4

C: CEREBLON ISOFORM 4

D: CEREBLON ISOFORM 4

hetero molecules

55.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CEREBLON ISOFORM 4

hetero molecules

defined by author&software
14 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CEREBLON ISOFORM 4

hetero molecules

defined by author&software
14 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: CEREBLON ISOFORM 4

hetero molecules

defined by author&software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: CEREBLON ISOFORM 4

hetero molecules

defined by author&software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	137.860, 137.860, 154.390
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	21 - 47
2	1	1	5	B	21 - 47
3	1	1	5	C	21 - 47
1	1	2	5	A	58 - 999
2	1	2	5	B	58 - 999
3	1	2	5	C	58 - 999
1	1	3	5	A	21 - 38
2	1	3	5	B	21 - 38
3	1	3	5	C	21 - 38
4	1	3	5	D	21 - 38
1	1	4	5	A	59 - 71
2	1	4	5	B	59 - 71
3	1	4	5	C	59 - 71
4	1	4	5	D	59 - 71
1	1	5	5	A	86 - 100
2	1	5	5	B	86 - 100
3	1	5	5	C	86 - 100
4	1	5	5	D	86 - 100
1	1	6	5	A	109 - 999
2	1	6	5	B	109 - 999
3	1	6	5	C	109 - 999
4	1	6	5	D	109 - 999

NCS ensembles :

ID
1
2
3
4
5
6

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.437259, 0.774496, -0.457121), (-0.335965, -0.330816, -0.881866), (-0.834225, 0.539181, 0.115551)	18.46928, -66.62801, -6.11625
3	given	(-0.479629, 0.498432, 0.722165), (-0.877357, -0.285722, -0.385497), (0.014194, -0.818492, 0.574343)	-21.55618, -84.74525, -33.11204
4	given	(-0.845968, 0.08599, 0.526255), (0.533234, 0.134801, 0.835159), (0.000876, 0.987134, -0.15989)	-44.82836, -2.57898, 20.00475

#1: Protein	CEREBLON ISOFORM 4 Mass: 13703.577 Da / Num. of mol.: 4 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.: 4 / 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 / Comment: medication*YM
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.8 Å³/Da / Density % sol: 68 % / Description: NONE
Crystal grow	Details: 64 MM SODIUM CITRATE PH 7.0, 100 MM HEPES PH 7.0, 10 %(W/V) PEG 5000 MME

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→39 Å / Num. obs: 19746 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 2.97 % / R_merge(I) obs: 0.1 / Net I/σ(I): 10.53
Reflection shell	Resolution: 2.9→3.07 Å / Redundancy: 2.95 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 2.22 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V2Y

4v2y

Resolution: 2.9→38.98 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.924 / SU B: 24.246 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21688	989	5 %	RANDOM
R_work	0.17452	-	-	-
obs	0.17664	18776	99.65 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 48.624 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.65 Å²	-0.32 Å²	0 Å²
2-	-	-0.65 Å²	0 Å²
3-	-	-	2.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→38.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3308	0	46	0	3354

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	3525
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3173
X-RAY DIFFRACTION	r_angle_refined_deg	1.952	1.928	4777
X-RAY DIFFRACTION	r_angle_other_deg	1.038	3	7267
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.979	5	427
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.633	21.951	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.674	15	509
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.071	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	458
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	4073
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	957
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.759	2.702	1717
X-RAY DIFFRACTION	r_mcbond_other	1.758	2.701	1716
X-RAY DIFFRACTION	r_mcangle_it	2.846	4.045	2141
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.144	2.898	1808
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	158	medium positional	0.2	0.5
1	2	B	158	medium positional	0.19	0.5
1	3	C	158	medium positional	0.15	0.5
2	1	A	376	medium positional	0.29	0.5
2	2	B	376	medium positional	0.22	0.5
2	3	C	376	medium positional	0.25	0.5
3	1	A	107	medium positional	0.18	0.5
3	2	B	107	medium positional	0.21	0.5
3	3	C	107	medium positional	0.18	0.5
3	4	D	107	medium positional	0.32	0.5
4	1	A	70	medium positional	0.22	0.5
4	2	B	70	medium positional	0.28	0.5
4	3	C	70	medium positional	0.28	0.5
4	4	D	70	medium positional	0.61	0.5
5	1	A	87	medium positional	0.18	0.5
5	2	B	87	medium positional	0.2	0.5
5	3	C	87	medium positional	0.19	0.5
5	4	D	87	medium positional	0.26	0.5
6	1	A	87	medium positional	0.31	0.5
6	2	B	87	medium positional	0.28	0.5
6	3	C	87	medium positional	0.34	0.5
6	4	D	87	medium positional	0.44	0.5
1	1	A	278	loose positional	0.5	5
1	2	B	278	loose positional	0.79	5
1	3	C	278	loose positional	0.51	5
2	1	A	581	loose positional	0.91	5
2	2	B	581	loose positional	0.87	5
2	3	C	581	loose positional	1.08	5
3	1	A	205	loose positional	0.51	5
3	2	B	205	loose positional	0.95	5
3	3	C	205	loose positional	0.51	5
3	4	D	205	loose positional	0.67	5
4	1	A	118	loose positional	0.87	5
4	2	B	118	loose positional	1.56	5
4	3	C	118	loose positional	0.8	5
4	4	D	118	loose positional	1.32	5
5	1	A	121	loose positional	0.63	5
5	2	B	121	loose positional	0.48	5
5	3	C	121	loose positional	0.45	5
5	4	D	121	loose positional	0.61	5
6	1	A	145	loose positional	0.84	5
6	2	B	145	loose positional	0.6	5
6	3	C	145	loose positional	0.66	5
6	4	D	145	loose positional	1.05	5
1	1	A	158	medium thermal	3.89	2
1	2	B	158	medium thermal	3.56	2
1	3	C	158	medium thermal	2.54	2
2	1	A	376	medium thermal	2.83	2
2	2	B	376	medium thermal	2.53	2
2	3	C	376	medium thermal	3.4	2
3	1	A	107	medium thermal	2.33	2
3	2	B	107	medium thermal	2.69	2
3	3	C	107	medium thermal	3.36	2
3	4	D	107	medium thermal	4.43	2
4	1	A	70	medium thermal	2.46	2
4	2	B	70	medium thermal	3.18	2
4	3	C	70	medium thermal	2.52	2
4	4	D	70	medium thermal	2.52	2
5	1	A	87	medium thermal	1.84	2
5	2	B	87	medium thermal	1.93	2
5	3	C	87	medium thermal	3.17	2
5	4	D	87	medium thermal	2.09	2
6	1	A	87	medium thermal	4.53	2
6	2	B	87	medium thermal	2.25	2
6	3	C	87	medium thermal	3.15	2
6	4	D	87	medium thermal	3.91	2
1	1	A	278	loose thermal	4.08	10
1	2	B	278	loose thermal	3.75	10
1	3	C	278	loose thermal	3.58	10
2	1	A	581	loose thermal	3.92	10
2	2	B	581	loose thermal	4.32	10
2	3	C	581	loose thermal	3.84	10
3	1	A	205	loose thermal	4.23	10
3	2	B	205	loose thermal	3.77	10
3	3	C	205	loose thermal	4.22	10
3	4	D	205	loose thermal	6.42	10
4	1	A	118	loose thermal	4.36	10
4	2	B	118	loose thermal	6.42	10
4	3	C	118	loose thermal	2.98	10
4	4	D	118	loose thermal	4.5	10
5	1	A	121	loose thermal	3.76	10
5	2	B	121	loose thermal	3.19	10
5	3	C	121	loose thermal	3.75	10
5	4	D	121	loose thermal	3.62	10
6	1	A	145	loose thermal	5.63	10
6	2	B	145	loose thermal	2.35	10
6	3	C	145	loose thermal	3.49	10
6	4	D	145	loose thermal	5.82	10

LS refinement shell

Resolution: 2.899→2.973 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.323	70	-
R_work	0.276	1331	-
obs	-	-	98.38 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	5.1611	-1.3138	3.3924	1.8059	-0.5736	5.666	-0.2184	0.1831	0.4608	-0.0683	0.0567	-0.2509	-0.5383	0.3899	0.1617	0.0756	-0.0518	-0.0166	0.0817	0.0137	0.086	-14.3684	-24.7646	3.7597
2	3.8852	1.1218	0.4421	5.2168	1.2928	2.9092	-0.2085	0.6564	-0.1187	-0.8042	0.1854	0.0472	0.0052	0.1372	0.0231	0.2076	-0.083	-0.0313	0.1627	0.0007	0.0158	-36.582	-34.0171	-20.9563
3	5.1334	1.3289	-2.4469	4.8112	0.0044	3.7474	0.3076	-0.7139	0.7075	0.803	-0.3208	0.921	0.0885	-0.1486	0.0132	0.3005	-0.1124	0.1163	0.229	-0.182	0.2811	-55.8101	-43.829	3.2301
4	1.0844	0.275	-0.6336	5.9686	1.0404	2.7108	-0.0387	-0.0372	0.0909	0.3638	0.0685	0.1075	-0.0567	0.1925	-0.0298	0.0539	-0.0221	-0.0252	0.0302	0.0246	0.0504	-39.9557	-17.1625	0.2678

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 151
2	X-RAY DIFFRACTION	2	B	19 - 151
3	X-RAY DIFFRACTION	3	C	19 - 151
4	X-RAY DIFFRACTION	4	D	14 - 150

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