PDB-3dry: X-ray crystal structure of human KCTD5 protein crystallized in lo...

ID or keywords:

Entry

Database: PDB / ID: 3dry

Title

X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer

Components

BTB/POZ domain-containing protein KCTD5

Keywords

UNKNOWN FUNCTION / KCTD5 / BTB/POZ / Golgi / GRASP55 / potassium channel DOMAIN T1 / PENTAMERIC ASSEMBLY / Host-virus interaction / Nucleus

Function / homology

Function and homology information

Cul3-RING ubiquitin ligase complex / cullin family protein binding / protein homooligomerization / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Tereshko, V. / Dementieva, I. / Goldstein, S.A.N.

Citation

Journal: J.Mol.Biol. / Year: 2009
Title: Pentameric assembly of potassium channel tetramerization domain-containing protein 5.
Authors: Dementieva, I.S. / Tereshko, V. / McCrossan, Z.A. / Solomaha, E. / Araki, D. / Xu, C. / Grigorieff, N. / Goldstein, S.A.

History

Deposition	Jul 11, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3dry.cif.gz	174.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3dry.ent.gz	139.2 KB	Display	PDB format
PDBx/mmJSON format	3dry.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3dry_validation.pdf.gz	469.9 KB	Display	wwPDB validaton report
Full document	3dry_full_validation.pdf.gz	508.3 KB	Display
Data in XML	3dry_validation.xml.gz	33.4 KB	Display
Data in CIF	3dry_validation.cif.gz	44.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/3dry ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3dry	HTTPS FTP

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Related structure data

Related structure data	3drxSC 3drzC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6e97-d 3drx-d 3d12-1 1pg3-d 2xew-d 1o57-d 1pg4-d 3rg2-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1)

Deposited unit

A: BTB/POZ domain-containing protein KCTD5

B: BTB/POZ domain-containing protein KCTD5

C: BTB/POZ domain-containing protein KCTD5

D: BTB/POZ domain-containing protein KCTD5

E: BTB/POZ domain-containing protein KCTD5

115 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	102.990, 106.791, 110.174
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E
1	3	A
2	3	B
3	3	C
4	3	D
5	3	E

NCS domain segments:

Refine code: 4

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	TRP	TRP	ASP	ASP	A	A	45 - 95	13 - 63
2	1	1	TRP	TRP	ASP	ASP	B	B	45 - 95	13 - 63
3	1	1	TRP	TRP	ASP	ASP	C	C	45 - 95	13 - 63
4	1	1	TRP	TRP	ASP	ASP	D	D	45 - 95	13 - 63
5	1	1	TRP	TRP	ASP	ASP	E	E	45 - 95	13 - 63
1	1	2	PRO	PRO	ARG	ARG	A	A	96 - 145	64 - 113
2	1	2	PRO	PRO	ARG	ARG	B	B	96 - 145	64 - 113
3	1	2	PRO	PRO	ARG	ARG	C	C	96 - 145	64 - 113
4	1	2	PRO	PRO	ARG	ARG	D	D	96 - 145	64 - 113
5	1	2	PRO	PRO	ARG	ARG	E	E	96 - 145	64 - 113
1	1	3	LYS	LYS	ILE	ILE	A	A	155 - 187	123 - 155
2	1	3	LYS	LYS	ILE	ILE	B	B	155 - 187	123 - 155
3	1	3	LYS	LYS	ILE	ILE	C	C	155 - 187	123 - 155
4	1	3	LYS	LYS	ILE	ILE	D	D	155 - 187	123 - 155
5	1	3	LYS	LYS	ILE	ILE	E	E	155 - 187	123 - 155
1	2	3	GLU	GLU	HIS	HIS	A	A	200 - 210	168 - 178
2	2	3	GLU	GLU	HIS	HIS	B	B	200 - 210	168 - 178
3	2	3	GLU	GLU	HIS	HIS	C	C	200 - 210	168 - 178
4	2	3	GLU	GLU	HIS	HIS	D	D	200 - 210	168 - 178
5	2	3	GLU	GLU	HIS	HIS	E	E	200 - 210	168 - 178

NCS ensembles :

ID
1
2
3

#1: Protein	BTB/POZ domain-containing protein KCTD5 Mass: 23041.953 Da / Num. of mol.: 5 / Fragment: UNP residues 34-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: MODIFIED VECTOR, TEV PROTEASE CLEAVAGE SITE REPLACING THROMBIN SITE Gene: KCTD5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NXV2

#1: Protein

BTB/POZ domain-containing protein KCTD5

Mass: 23041.953 Da / Num. of mol.: 5 / Fragment: UNP residues 34-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human)
Description: MODIFIED VECTOR, TEV PROTEASE CLEAVAGE SITE REPLACING THROMBIN SITE
Gene: KCTD5 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9NXV2

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.22 %
Crystal grow	Method: vapor diffusion / pH: 7.5 Details: 0.2 M proline, 100 mM HEPES, 7% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97915 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS K-B GEOMETRY
Radiation	Monochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 3.3→50 Å / Num. obs: 20180 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / R_merge(I) obs: 0.074 / Net I/σ(I): 18.14
Reflection shell	Resolution: 3.3→3.4 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1151 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3DRX

3drx

Resolution: 3.3→20 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.825 / SU B: 86.335 / SU ML: 0.636 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.738 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30791	1913	10.2 %	RANDOM
R_work	0.25257	-	-	-
all	0.26018	-	-	-
obs	0.26018	16774	99.7 %	-

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: 73.224 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.94 Å²	0 Å²	0 Å²
2-	-	-4.73 Å²	0 Å²
3-	-	-	13.67 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6810	0	0	0	6810

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	6940
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	4777
X-RAY DIFFRACTION	r_angle_refined_deg	1.276	1.973	9379
X-RAY DIFFRACTION	r_angle_other_deg	0.941	3.002	11638
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.843	5	835
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.47	24.497	338
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.233	15	1277
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.817	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1052
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7619
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1374
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	1839
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	5002
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	3279
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	3687
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	196
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.07	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.196	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.213	0.2	59
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.21	0.2	6
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	0.373	1.5	5472
X-RAY DIFFRACTION	r_mcbond_other	0.051	1.5	1700
X-RAY DIFFRACTION	r_mcangle_it	0.428	2	6810
X-RAY DIFFRACTION	r_scbond_it	0.478	3	3191
X-RAY DIFFRACTION	r_scangle_it	0.743	4.5	2569
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	714	medium positional	0.33	0.5
1	2	B	714	medium positional	0.38	0.5
1	3	C	714	medium positional	0.51	0.5
1	4	D	714	medium positional	0.44	0.5
1	5	E	714	medium positional	0.43	0.5
2	1	A	709	medium positional	0.32	0.5
2	2	B	709	medium positional	0.31	0.5
2	3	C	709	medium positional	0.32	0.5
2	4	D	709	medium positional	0.37	0.5
2	5	E	709	medium positional	0.33	0.5
3	1	A	598	medium positional	0.55	0.5
3	2	B	598	medium positional	0.47	0.5
3	3	C	598	medium positional	0.48	0.5
3	4	D	598	medium positional	0.49	0.5
3	5	E	598	medium positional	0.47	0.5
1	1	A	714	medium thermal	0.17	2
1	2	B	714	medium thermal	0.22	2
1	3	C	714	medium thermal	0.27	2
1	4	D	714	medium thermal	0.31	2
1	5	E	714	medium thermal	0.2	2
2	1	A	709	medium thermal	0.15	2
2	2	B	709	medium thermal	0.15	2
2	3	C	709	medium thermal	0.18	2
2	4	D	709	medium thermal	0.22	2
2	5	E	709	medium thermal	0.16	2
3	1	A	598	medium thermal	0.26	2
3	2	B	598	medium thermal	0.22	2
3	3	C	598	medium thermal	0.25	2
3	4	D	598	medium thermal	0.18	2
3	5	E	598	medium thermal	0.18	2

LS refinement shell

Resolution: 3.3→3.383 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.415	140	-
R_work	0.361	1151	-
obs	-	-	98.47 %

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	4.2319	-0.2036	-0.1425	3.5736	0.1552	0.8118	-0.0382	-0.6276	-0.2981	0.4279	0.0365	0.5241	0.0643	0.0164	0.0017	-0.2308	-0.0161	0.1036	-0.2114	0.0053	-0.8865	14.0071	12.0171	26.795
2	3.4602	-0.91	0.0222	4.0712	-0.0755	0.5133	0.0993	0.739	-0.4566	-0.8648	-0.3136	0.7033	-0.0479	-0.1714	0.2143	0.002	0.021	-0.1112	-0.0353	-0.0566	-0.6647	6.9964	10.7935	7.7206
3	6.3021	-2.275	-1.8384	5.8687	1.0636	2.3121	0.171	0.334	-0.2374	-0.1128	-0.0193	-0.087	0.2033	0.03	-0.1517	-0.1096	0.0462	-0.105	-0.0261	-0.1814	-0.8354	-6.6996	9.5422	-36.7865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	40 - 95	8 - 63
2	X-RAY DIFFRACTION	1	B	B	42 - 95	10 - 63
3	X-RAY DIFFRACTION	1	C	C	33 - 95	1 - 63
4	X-RAY DIFFRACTION	1	D	D	34 - 95	2 - 63
5	X-RAY DIFFRACTION	1	E	E	42 - 95	10 - 63
6	X-RAY DIFFRACTION	2	A	A	96 - 150	64 - 118
7	X-RAY DIFFRACTION	2	B	B	96 - 150	64 - 118
8	X-RAY DIFFRACTION	2	C	C	96 - 150	64 - 118
9	X-RAY DIFFRACTION	2	D	D	96 - 150	64 - 118
10	X-RAY DIFFRACTION	2	E	E	96 - 150	64 - 118
11	X-RAY DIFFRACTION	3	A	A	151 - 210	119 - 178
12	X-RAY DIFFRACTION	3	B	B	151 - 210	119 - 178
13	X-RAY DIFFRACTION	3	C	C	151 - 210	119 - 178
14	X-RAY DIFFRACTION	3	D	D	151 - 210	119 - 178
15	X-RAY DIFFRACTION	3	E	E	151 - 210	119 - 178

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