PDB-6r60: asymmetric antiparallel assembly of two 5-bladed beta-propeller f...

ID or keywords:

Entry

Database: PDB / ID: 6r60

Title

asymmetric antiparallel assembly of two 5-bladed beta-propeller fragments

Components

WD-40 repeat protein

Keywords

UNKNOWN FUNCTION / Repeat Protein / Fragment Amplification / Protein Evolution / Protein Design / WD40

Function / homology

Function and homology information

microtubule organizing center organization / microtubule plus-end binding / retrograde axonal transport / microtubule associated complex / dynein complex binding / cytoplasmic microtubule / kinetochore / neuron projection / neuronal cell body / membrane / metal ion binding
Similarity search - Function

Biological species

Nostoc punctiforme (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Afanasieva, E. / Lupas, A.N. / Hartmann, M.D.

Citation

Journal: Elife / Year: 2019
Title: Structural diversity of oligomeric beta-propellers with different numbers of identical blades.
Authors: Afanasieva, E. / Chaudhuri, I. / Martin, J. / Hertle, E. / Ursinus, A. / Alva, V. / Hartmann, M.D. / Lupas, A.N.

History

Deposition	Mar 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	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 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6r60.cif.gz	301.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6r60.ent.gz	247.5 KB	Display	PDB format
PDBx/mmJSON format	6r60.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6r60_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	6r60_full_validation.pdf.gz	448.1 KB	Display
Data in XML	6r60_validation.xml.gz	34.3 KB	Display
Data in CIF	6r60_validation.cif.gz	51.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r6/6r60 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r60	HTTPS FTP

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Related structure data

Related structure data	6r5xC 6r5yC 6r5zC 2ymuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1td6-d 3wcg-5 3lee-1 3vja-1 3weh-d 3wcc-2 3vj8-d 3eu7-d 3wek-d 3lee-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: WD-40 repeat protein

B: WD-40 repeat protein

C: WD-40 repeat protein

D: WD-40 repeat protein

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

1

A: WD-40 repeat protein

B: WD-40 repeat protein

defined by author&software
Evidence: gel filtration
44.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: WD-40 repeat protein

D: WD-40 repeat protein

defined by author&software
44.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.754, 107.519, 179.187
Angle α, β, γ (deg.)	90.00, 94.40, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-470- HOH
2	1	C-462- HOH
3	1	C-478- HOH
4	1	D-389- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-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	ARG	ARG	LEU	LEU	A	A	32 - 204	34 - 206
2	1	ARG	ARG	LEU	LEU	B	B	32 - 204	34 - 206
1	2	TRP	TRP	THR	THR	A	A	7 - 205	9 - 207
2	2	TRP	TRP	THR	THR	C	C	7 - 205	9 - 207
1	3	ARG	ARG	LEU	LEU	A	A	32 - 204	34 - 206
2	3	ARG	ARG	LEU	LEU	D	D	32 - 204	34 - 206
1	4	ARG	ARG	LEU	LEU	B	B	32 - 204	34 - 206
2	4	ARG	ARG	LEU	LEU	C	C	32 - 204	34 - 206
1	5	ARG	ARG	LEU	LEU	B	B	32 - 204	34 - 206
2	5	ARG	ARG	LEU	LEU	D	D	32 - 204	34 - 206
1	6	ARG	ARG	LEU	LEU	C	C	32 - 204	34 - 206
2	6	ARG	ARG	LEU	LEU	D	D	32 - 204	34 - 206

NCS ensembles :

ID
6
1
2
3
4
5

#1: Protein	WD-40 repeat protein / asymmetric antiparallel assembly of two 5-bladed beta-propeller fragments Mass: 22133.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: Npun_R6612 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J0I0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 42.96 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M Magnesium chloride, 0.1 M HEPES pH 7, 15%(w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→37.2 Å / Num. obs: 74436 / % possible obs: 98.1 % / Redundancy: 3.31 % / CC_1/2: 0.995 / R_merge(I) obs: 0.088 / Net I/σ(I): 9.17
Reflection shell	Resolution: 1.75→1.85 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.454 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 11645 / CC_1/2: 0.848 / % possible all: 95.3

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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: 2YMU

2ymu

Resolution: 1.75→37.2 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.928 / SU B: 7.231 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24035	3752	5 %	RANDOM
R_work	0.19801	-	-	-
obs	0.20011	70952	98.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 26.931 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.03 Å²	-0 Å²	0.29 Å²
2-	-	-1.56 Å²	-0 Å²
3-	-	-	0.48 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→37.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5608	0	0	691	6299

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	5762
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	5300
X-RAY DIFFRACTION	r_angle_refined_deg	1.53	1.909	7866
X-RAY DIFFRACTION	r_angle_other_deg	1.481	3	12174
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.847	5	752
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.044	25.602	241
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.027	15	903
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.774	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	903
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6739
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1369
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	0.942	1.397	2999
X-RAY DIFFRACTION	r_mcbond_other	0.939	1.397	2998
X-RAY DIFFRACTION	r_mcangle_it	1.418	2.09	3745
X-RAY DIFFRACTION	r_mcangle_other	1.418	2.09	3746
X-RAY DIFFRACTION	r_scbond_it	1.223	1.566	2763
X-RAY DIFFRACTION	r_scbond_other	1.222	1.566	2764
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.926	2.291	4119
X-RAY DIFFRACTION	r_long_range_B_refined	6.587	13.232	6831
X-RAY DIFFRACTION	r_long_range_B_other	6.447	12.4	6579
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	8779	0.14
1	2	B	8779	0.14
2	1	A	11367	0.09
2	2	C	11367	0.09
3	1	A	8762	0.15
3	2	D	8762	0.15
4	1	B	8791	0.14
4	2	C	8791	0.14
5	1	B	9892	0.09
5	2	D	9892	0.09
6	1	C	8832	0.14
6	2	D	8832	0.14

LS refinement shell

Resolution: 1.75→1.795 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.374	296	-
R_work	0.378	5325	-
obs	-	-	99.95 %

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	1.9436	-1.7543	0.3942	7.6377	-0.7215	2.3098	0.0334	-0.0807	-0.0894	-0.1254	-0.0753	0.1624	0.0285	-0.1054	0.0419	0.1463	0.0001	-0.0132	0.0763	0.0192	0.0752	23.6522	37.6621	9.0158
2	2.1478	0.0382	0.6666	6.0595	-0.7296	3.1772	-0.0901	0.3805	0.1417	-0.3593	0.0244	-0.1604	-0.0543	0.068	0.0657	0.0822	-0.0129	0.0035	0.0687	0.0204	0.0843	29.9113	28.8344	14.5245
3	1.0262	0.2663	0.5428	5.4419	0.25	3.0733	-0.0422	0.0368	0.0442	-0.0751	0.0433	-0.1413	0.0749	0.276	-0.0011	0.038	0.0168	0.0168	0.0286	0.0093	0.0638	31.6449	25.45	25.9275
4	2.2007	1.8493	-0.4421	4.1621	-0.1868	3.7244	-0.1011	-0.0169	-0.1463	0.2317	0.0398	-0.0521	0.0965	0.2389	0.0613	0.0829	0.0266	0.0153	0.0233	-0.0017	0.0541	27.2134	29.3031	36.3345
5	2.1683	0.2098	-1.5915	3.034	0.5962	3.4293	-0.1199	-0.0667	-0.0279	0.0674	0.0331	0.0112	-0.0613	-0.0119	0.0869	0.0775	0.0366	0.0086	0.0201	-0.0075	0.0575	20.1238	38.5726	39.0946
6	6.9768	6.5563	-3.4283	16.1399	-4.9746	11.325	-0.409	0.9839	0.1413	-0.4795	0.4703	-0.1603	0.2646	0.4228	-0.0613	0.1811	0.0516	-0.0135	0.3009	-0.002	0.2197	21.0811	46.4425	27.363
7	2.3275	-0.6698	-0.5367	7.5309	1.2953	4.3542	-0.0064	-0.0787	-0.2214	0.0381	0.0399	0.157	0.2584	-0.0523	-0.0335	0.1327	0.0057	-0.0121	0.0413	-0.011	0.0742	13.8585	45.3244	8.7718
8	1.1422	0.5212	0.0039	5.8512	0.4499	4.2526	-0.1539	0.2265	-0.0668	-0.5575	0.0839	0.2445	0.135	-0.2136	0.07	0.0863	-0.0343	0.0043	0.0566	-0.0105	0.0781	8.9591	54.9834	14.7389
9	0.7456	0.822	-0.0257	4.4916	0.3151	4.1967	-0.0212	-0.1111	-0.0383	-0.0499	-0.0782	0.2256	0.0263	-0.3588	0.0994	0.0205	0.003	0.0276	0.0498	0.0064	0.0634	10.0656	58.6727	26.0944
10	0.5962	1.3655	0.829	5.6317	-0.4532	5.9608	-0.0378	-0.0146	-0.0613	0.1122	-0.0226	-0.1772	0.3332	0.1207	0.0604	0.134	0.0352	0.0258	0.01	0.0057	0.0506	17.3173	54.3154	35.0706
11	1.4585	1.9911	-0.7629	7.4795	-1.1312	2.8574	0.0117	0.1182	0.0966	-0.1105	0.0377	0.0396	-0.0423	-0.1177	-0.0494	0.0955	-0.0069	0.0253	0.0968	0.0012	0.0922	18.2458	65.7452	80.8243
12	1.1026	1.2709	-1.6054	3.1125	-0.0529	4.6645	0.1046	-0.1681	-0.104	0.3737	-0.1079	-0.1632	0.0279	0.1302	0.0033	0.1055	0.0469	0.0263	0.153	0.0464	0.1348	25.5064	74.2826	76.2193
13	1.8169	-0.1058	-0.7326	4.9821	-0.3924	2.2083	0.0047	-0.1152	-0.0638	0.0227	0.0327	-0.1905	-0.0816	0.2368	-0.0374	0.0473	-0.0113	0.0233	0.031	-0.0201	0.0745	29.0637	76.8508	64.9851
14	2.5223	-0.3778	1.3797	4.3027	0.1258	3.7087	-0.171	0.0907	0.1337	-0.1612	0.2253	-0.2738	-0.222	0.3793	-0.0543	0.0722	-0.023	0.0379	0.0506	-0.0186	0.0597	26.307	72.356	54.3311
15	1.9894	-0.842	0.9565	3.4018	1.376	5.9769	0.0175	0.114	-0.0283	-0.0025	0.0662	-0.0421	0.2001	0.1591	-0.0836	0.0569	-0.0039	0.0061	0.0122	-0.0023	0.0579	19.5702	63.1484	50.946
16	4.1501	-2.6745	0.1911	9.6145	-5.4126	11.0415	-0.1032	-0.5624	0.2109	0.2361	0.0468	-0.1641	-0.2368	0.4544	0.0564	0.1583	-0.0564	0.002	0.1222	-0.03	0.142	18.3392	55.8529	62.7474
17	2.3358	1.2274	-0.6726	7.7207	0.8375	3.9214	0.0421	-0.0195	0.1799	-0.1919	-0.0397	0.1452	-0.1309	-0.1162	-0.0025	0.0791	0.0073	0.0137	0.066	-0.0151	0.0669	8.458	58.0437	79.8689
18	0.2084	0.5427	-0.2026	5.4459	0.9708	4.4454	-0.0178	-0.1568	0.0825	0.3986	-0.0926	0.3988	-0.0471	-0.3439	0.1104	0.0632	0.084	0.0067	0.2458	-0.0631	0.0913	4.6362	48.0652	73.5181
19	0.6397	-0.3074	0.3016	3.8989	0.064	4.0602	0.0303	0.0744	-0.0934	-0.006	-0.1112	0.2848	0.0892	-0.3194	0.0809	0.0129	-0.0034	0.0033	0.0421	-0.0216	0.0667	7.3322	43.6538	62.7778
20	0.3722	-0.8314	-1.1807	3.9379	0.8853	5.4985	0.0499	0.0212	0.0081	-0.1767	-0.0876	-0.0135	-0.1956	0.0477	0.0377	0.0424	-0.0206	-0.0003	0.0288	0.0145	0.0637	15.3214	47.4037	54.5532

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 42
2	X-RAY DIFFRACTION	2	A	43 - 83
3	X-RAY DIFFRACTION	3	A	84 - 124
4	X-RAY DIFFRACTION	4	A	125 - 165
5	X-RAY DIFFRACTION	5	A	166 - 9999
6	X-RAY DIFFRACTION	6	B	-10 - 48
7	X-RAY DIFFRACTION	7	B	49 - 83
8	X-RAY DIFFRACTION	8	B	84 - 124
9	X-RAY DIFFRACTION	9	B	125 - 165
10	X-RAY DIFFRACTION	10	B	166 - 9999
11	X-RAY DIFFRACTION	11	C	-10 - 42
12	X-RAY DIFFRACTION	12	C	43 - 83
13	X-RAY DIFFRACTION	13	C	84 - 124
14	X-RAY DIFFRACTION	14	C	125 - 165
15	X-RAY DIFFRACTION	15	C	166 - 9999
16	X-RAY DIFFRACTION	16	D	-10 - 48
17	X-RAY DIFFRACTION	17	D	49 - 83
18	X-RAY DIFFRACTION	18	D	84 - 124
19	X-RAY DIFFRACTION	19	D	125 - 165
20	X-RAY DIFFRACTION	20	D	166 - 9999

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