PDB-3drx: X-ray crystal structure of human KCTD5 protein crystallized in hi...

ID or keywords:

Entry

Database: PDB / ID: 3drx

Title

X-ray crystal structure of human KCTD5 protein crystallized in high-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 /

SAD / Resolution: 3.11 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	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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	3drx.cif.gz	178.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3drx_validation.pdf.gz	464.1 KB	Display	wwPDB validaton report
Full document	3drx_full_validation.pdf.gz	497.4 KB	Display
Data in XML	3drx_validation.xml.gz	37.8 KB	Display
Data in CIF	3drx_validation.cif.gz	47.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/3drx ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3drx	HTTPS FTP

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Related structure data

Related structure data	3dryC 3drzC C: citing same article (ref.)
Similar structure data	6hla-d 5xf9-2 6hl2-d 1p4a-d 6vlg-2 5xfa-2 3dry-d 5xf9-1 20238 1ma1-d 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)	72.862, 128.583, 152.524
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	ARG	ARG	A	A	45 - 72	13 - 40
2	1	1	TRP	TRP	ARG	ARG	B	B	45 - 72	13 - 40
3	1	1	TRP	TRP	ARG	ARG	C	C	45 - 72	13 - 40
4	1	1	TRP	TRP	ARG	ARG	D	D	45 - 72	13 - 40
5	1	1	TRP	TRP	ARG	ARG	E	E	45 - 72	13 - 40
1	2	1	GLY	GLY	ASP	ASP	A	A	88 - 95	56 - 63
2	2	1	GLY	GLY	ASP	ASP	B	B	88 - 95	56 - 63
3	2	1	GLY	GLY	ASP	ASP	C	C	88 - 95	56 - 63
4	2	1	GLY	GLY	ASP	ASP	D	D	88 - 95	56 - 63
5	2	1	GLY	GLY	ASP	ASP	E	E	88 - 95	56 - 63
1	1	2	PRO	PRO	SER	SER	A	A	96 - 150	64 - 118
2	1	2	PRO	PRO	SER	SER	B	B	96 - 150	64 - 118
3	1	2	PRO	PRO	SER	SER	C	C	96 - 150	64 - 118
4	1	2	PRO	PRO	SER	SER	D	D	96 - 150	64 - 118
5	1	2	PRO	PRO	SER	SER	E	E	96 - 150	64 - 118
1	1	3	LYS	LYS	VAL	VAL	A	A	155 - 185	123 - 153
2	1	3	LYS	LYS	VAL	VAL	B	B	155 - 185	123 - 153
3	1	3	LYS	LYS	VAL	VAL	C	C	155 - 185	123 - 153
4	1	3	LYS	LYS	VAL	VAL	D	D	155 - 185	123 - 153
5	1	3	LYS	LYS	VAL	VAL	E	E	155 - 185	123 - 153
1	2	3	PHE	PHE	HIS	HIS	A	A	201 - 210	169 - 178
2	2	3	PHE	PHE	HIS	HIS	B	B	201 - 210	169 - 178
3	2	3	PHE	PHE	HIS	HIS	C	C	201 - 210	169 - 178
4	2	3	PHE	PHE	HIS	HIS	D	D	201 - 210	169 - 178
5	2	3	PHE	PHE	HIS	HIS	E	E	201 - 210	169 - 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
Has protein modification	Y

#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

Has protein modification

Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.1 Å³/Da / Density % sol: 60.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: 3.2 M NaCl, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97936 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: 0.97936 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 26106 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / R_merge(I) obs: 0.066 / Net I/σ(I): 15.62
Reflection shell	Resolution: 3.1→3.21 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.4.0073	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.11→20 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.856 / SU B: 45.413 / SU ML: 0.361 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.275	1321	5.1 %	RANDOM
R_work	0.227	-	-	-
obs	0.23	24665	98.9 %	-
all	-	24665	-	-

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: 67.02 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.23 Å²	0 Å²	0 Å²
2-	-	-0.66 Å²	0 Å²
3-	-	-	2.88 Å²

Refinement step

Cycle: LAST / Resolution: 3.11→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6907	0	0	0	6907

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	7045
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.046	1.97	9521
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.252	5	848
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.569	24.36	344
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.984	15	1288
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.874	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	1065
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5274
X-RAY DIFFRACTION	r_gen_planes_other
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	0.61	1.5	4260
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.165	2	6903
X-RAY DIFFRACTION	r_scbond_it	1.276	3	2785
X-RAY DIFFRACTION	r_scangle_it	2.268	4.5	2618
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	303	medium positional	0.58	0.5
1	1	B	303	medium positional	0.45	0.5
1	1	C	303	medium positional	0.36	0.5
1	1	D	303	medium positional	0.39	0.5
1	1	E	303	medium positional	0.47	0.5
2	2	A	448	medium positional	0.33	0.5
2	2	B	448	medium positional	0.33	0.5
2	2	C	448	medium positional	0.34	0.5
2	2	D	448	medium positional	0.34	0.5
2	2	E	448	medium positional	0.33	0.5
3	3	A	341	medium positional	0.51	0.5
3	3	B	341	medium positional	0.64	0.5
3	3	C	341	medium positional	0.71	0.5
3	3	D	341	medium positional	0.71	0.5
3	3	E	341	medium positional	0.59	0.5
1	1	A	303	medium thermal	0.84	2
1	1	B	303	medium thermal	1.02	2
1	1	C	303	medium thermal	0.79	2
1	1	D	303	medium thermal	0.97	2
1	1	E	303	medium thermal	1.58	2
2	2	A	448	medium thermal	0.28	2
2	2	B	448	medium thermal	0.37	2
2	2	C	448	medium thermal	0.23	2
2	2	D	448	medium thermal	0.25	2
2	2	E	448	medium thermal	0.25	2
3	3	A	341	medium thermal	0.49	2
3	3	B	341	medium thermal	0.55	2
3	3	C	341	medium thermal	0.68	2
3	3	D	341	medium thermal	0.62	2
3	3	E	341	medium thermal	0.53	2

LS refinement shell

Resolution: 3.11→3.19 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.357	83	-
R_work	0.285	1670	-
obs	-	-	93.69 %

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	3.0645	-1.4674	-1.9434	2.7939	2.9171	3.6444	-0.0749	-0.4246	-0.2264	0.3638	0.2686	-0.1853	0.4116	0.4166	-0.1937	-0.2758	0.0047	-0.0507	-0.3252	-0.0981	-0.2216	28.9187	69.3535	121.6118
2	2.2793	-0.8882	-1.4371	1.9977	2.0764	2.9437	0.0124	0.4412	-0.6356	0.0565	-0.5004	0.9013	0.7134	-0.9484	0.488	-0.1611	-0.1229	-0.0221	0.0158	-0.3179	0.1388	14.3553	61.8597	109.6878
3	5.3287	-0.9943	-1.1853	6.513	1.2861	3.9068	0.2422	0.2679	0.6832	-0.4221	-0.2943	-0.2026	-0.4634	0.1067	0.0521	-0.4139	0.0023	-0.0059	-0.2422	-0.0208	-0.4123	-20.6021	42.5855	85.6013

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	34 - 95	2 - 63
2	X-RAY DIFFRACTION	1	B	B	34 - 95	2 - 63
3	X-RAY DIFFRACTION	1	C	C	35 - 95	3 - 63
4	X-RAY DIFFRACTION	1	D	D	34 - 95	2 - 63
5	X-RAY DIFFRACTION	1	E	E	34 - 95	2 - 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 - 211	119 - 179
13	X-RAY DIFFRACTION	3	C	C	151 - 211	119 - 179
14	X-RAY DIFFRACTION	3	D	D	151 - 211	119 - 179
15	X-RAY DIFFRACTION	3	E	E	151 - 211	119 - 179

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