PDB-6r5z: 9-bladed beta-propeller formed by three 3-bladed fragments

ID or keywords:

Entry

Database: PDB / ID: 6r5z

Title

9-bladed beta-propeller formed by three 3-bladed fragments

Components

9-bladed beta-propeller formed by three 3-bladed fragments

Keywords

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

Function / homology

Function and homology information

protein polyubiquitination / metal ion binding / membrane
Similarity search - Function

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Martin, J. / 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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Download

PDBx/mmCIF format	6r5z.cif.gz	280.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6r5z.ent.gz	229.7 KB	Display	PDB format
PDBx/mmJSON format	6r5z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6r5z_validation.pdf.gz	465.9 KB	Display	wwPDB validaton report
Full document	6r5z_full_validation.pdf.gz	473.1 KB	Display
Data in XML	6r5z_validation.xml.gz	28.3 KB	Display
Data in CIF	6r5z_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r5/6r5z ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r5z	HTTPS FTP

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Related structure data

Related structure data	6r5xC 6r5yC 6r60C 2ymuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6tjb-d 6tjc-d 6g6o-2 5l37-d 6tjh-2 6y7o-2 6g6o-1 6tji-2 6tjh-1 6tje-d 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: 9-bladed beta-propeller formed by three 3-bladed fragments

B: 9-bladed beta-propeller formed by three 3-bladed fragments

C: 9-bladed beta-propeller formed by three 3-bladed fragments

D: 9-bladed beta-propeller formed by three 3-bladed fragments

E: 9-bladed beta-propeller formed by three 3-bladed fragments

F: 9-bladed beta-propeller formed by three 3-bladed fragments

80.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 9-bladed beta-propeller formed by three 3-bladed fragments

B: 9-bladed beta-propeller formed by three 3-bladed fragments

C: 9-bladed beta-propeller formed by three 3-bladed fragments

defined by author&software
Evidence: gel filtration
40.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: 9-bladed beta-propeller formed by three 3-bladed fragments

E: 9-bladed beta-propeller formed by three 3-bladed fragments

F: 9-bladed beta-propeller formed by three 3-bladed fragments

defined by author&software
40.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.549, 92.353, 61.432
Angle α, β, γ (deg.)	90.00, 94.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 7 - 125 / Label seq-ID: 9 - 127

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	9-bladed beta-propeller formed by three 3-bladed fragments Mass: 13413.693 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: B2J0I0*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.88 Å³/Da / Density % sol: 34.59 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium fluoride, 20 %(w/v) PEG 3350

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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: Mar 12, 2012
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→38.3 Å / Num. obs: 59988 / % possible obs: 99.2 % / Redundancy: 4.67 % / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.75→1.85 Å / Redundancy: 4.44 % / R_merge(I) obs: 0.89 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 9362 / CC_1/2: 0.65 / % possible all: 95.9

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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→38.3 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.955 / SU B: 6.642 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21173	3011	5 %	RANDOM
R_work	0.18521	-	-	-
obs	0.18653	56974	99.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 31.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.91 Å²	0 Å²	0.09 Å²
2-	-	0.35 Å²	-0 Å²
3-	-	-	0.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→38.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5357	0	0	302	5659

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.02	5472
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	5015
X-RAY DIFFRACTION	r_angle_refined_deg	1.722	1.911	7469
X-RAY DIFFRACTION	r_angle_other_deg	1.669	3	11514
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.895	5	708
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.322	25.708	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.453	15	844
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.388	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	852
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	6393
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	1288
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	1.257	1.291	2850
X-RAY DIFFRACTION	r_mcbond_other	1.253	1.29	2849
X-RAY DIFFRACTION	r_mcangle_it	1.963	1.926	3552
X-RAY DIFFRACTION	r_mcangle_other	1.963	1.927	3553
X-RAY DIFFRACTION	r_scbond_it	1.844	1.565	2622
X-RAY DIFFRACTION	r_scbond_other	1.842	1.565	2622
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.832	2.268	3916
X-RAY DIFFRACTION	r_long_range_B_refined	6.457	12.032	6098
X-RAY DIFFRACTION	r_long_range_B_other	6.443	11.799	6040
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	6639	0.08
1	2	B	6639	0.08
2	1	A	6469	0.09
2	2	C	6469	0.09
3	1	A	6565	0.09
3	2	D	6565	0.09
4	1	A	6556	0.08
4	2	E	6556	0.08
5	1	A	6432	0.1
5	2	F	6432	0.1
6	1	B	6486	0.09
6	2	C	6486	0.09
7	1	B	6567	0.09
7	2	D	6567	0.09
8	1	B	6574	0.09
8	2	E	6574	0.09
9	1	B	6489	0.1
9	2	F	6489	0.1
10	1	C	6564	0.09
10	2	D	6564	0.09
11	1	C	6510	0.1
11	2	E	6510	0.1
12	1	C	6592	0.09
12	2	F	6592	0.09
13	1	D	6518	0.09
13	2	E	6518	0.09
14	1	D	6535	0.1
14	2	F	6535	0.1
15	1	E	6630	0.09
15	2	F	6630	0.09

LS refinement shell

Resolution: 1.746→1.791 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	216	-
R_work	0.366	3842	-
obs	-	-	91.05 %

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	7.0708	-0.3798	-0.4201	5.5408	0.822	2.2669	-0.0157	0.085	0.124	-0.1631	0.0282	-0.1863	-0.1816	0.1762	-0.0125	0.1522	0.0161	0.0183	0.084	0.0152	0.0889	24.9188	0.7443	12.6244
2	4.1209	-0.4347	0.746	3.1516	0.7414	4.0218	0.0784	0.2335	-0.2775	-0.115	-0.0284	-0.0414	-0.0247	-0.0603	-0.05	0.1244	0.0056	0.0224	0.073	-0.0014	0.0538	13.8284	-2.9446	12.214
3	5.0634	0.1837	-0.5625	3.751	0.5464	4.6811	0.2166	0.3012	-0.0428	-0.2469	-0.0808	0.2885	-0.2847	-0.4353	-0.1358	0.1677	0.037	-0.0145	0.1476	0.008	0.0648	3.3566	3.764	11.803
4	7.5276	-0.3408	0.775	5.275	-2.192	2.0618	-0.0915	0.1644	-0.4081	-0.0095	0.1858	0.2327	0.2229	-0.3777	-0.0943	0.228	-0.0017	0.038	0.3395	0.033	0.1003	-2.8459	14.3518	15.1076
5	2.0085	0.191	1.3851	4.0136	-2.502	9.8694	-0.0575	0.0361	0.1719	0.1157	0.1955	0.3647	-0.2485	-1.0209	-0.138	0.1604	0.0532	0.0387	0.3231	0.0241	0.0535	-0.5956	25.7701	13.3995
6	5.7321	0.6797	1.516	3.0657	0.3846	2.7431	-0.0543	0.4575	0.2513	-0.1128	0.1387	-0.0212	-0.5091	-0.0437	-0.0844	0.2647	0.0279	0.0382	0.151	0.0358	0.022	10.2123	31.2859	10.9907
7	4.4967	-0.818	-2.7648	4.9998	-1.24	6.946	0.046	0.1636	0.2942	-0.0404	-0.054	0.0433	-0.5878	-0.0896	0.0081	0.252	-0.0413	0.009	0.1055	0.0027	0.0565	22.5399	31.8514	12.9434
8	3.5268	-1.0992	-2.4874	5.7406	-0.4888	8.6399	0.0975	-0.1369	0.2518	-0.0112	-0.1803	-0.4954	-0.4572	0.504	0.0828	0.1492	-0.0444	0.0076	0.1452	0.0565	0.082	31.143	23.9292	10.337
9	5.5256	-1.7702	-0.8004	7.8234	-1.0186	4.0933	0.0731	0.0951	0.0203	-0.2543	-0.0185	-0.2444	0.259	0.0149	-0.0546	0.1819	-0.0131	0.031	0.1114	-0.0015	0.0557	30.2496	11.7533	9.1252
10	6.8487	0.9298	0.5705	6.0582	2.4096	2.1413	-0.0188	0.1844	-0.2353	-0.0366	0.1875	-0.2017	-0.0339	0.2891	-0.1687	0.1953	0.0361	0.0113	0.2064	-0.0675	0.1693	50.4318	46.015	19.5166
11	4.674	0.4196	2.1903	3.219	2.1389	6.051	0.0462	0.2426	-0.5551	0.1308	0.113	-0.0516	0.2366	0.3252	-0.1591	0.1248	0.0014	0.0361	0.1117	-0.06	0.1113	38.9319	43.4508	18.8461
12	7.4124	-0.4825	-0.8846	4.1244	2.5011	5.5075	-0.0503	0.1597	-0.4166	-0.0083	-0.0278	0.3013	-0.12	-0.2688	0.0781	0.1696	0.0178	0.0228	0.0872	-0.0127	0.0938	29.3203	50.8794	18.2698
13	8.0447	-0.0094	1.2192	6.9615	-1.2239	1.4043	-0.0581	-0.2081	-0.2324	0.1453	0.0286	0.2205	0.1482	-0.0036	0.0295	0.181	0.007	0.0231	0.1215	-0.0089	0.0687	23.6978	61.8438	22.0359
14	3.1178	0.814	-0.0411	4.8782	-2.4173	5.0663	-0.0583	0.0991	0.0769	-0.0489	0.1843	0.3609	0.2053	-0.2261	-0.1259	0.1107	-0.0149	0.005	0.0469	0.0117	0.0279	26.9921	73.1232	19.9999
15	5.2595	1.4012	3.1226	5.4731	-0.62	4.5255	-0.0629	0.2824	0.103	-0.132	0.0992	-0.0298	-0.1062	0.17	-0.0363	0.1168	0.0027	0.0269	0.1127	0.0085	0.0128	38.3498	77.548	17.5439
16	3.8099	0.1783	-0.8372	6.5972	-0.099	3.34	-0.0691	0.2566	0.2527	-0.2458	0.0932	-0.053	-0.0871	-0.093	-0.0241	0.1304	-0.0448	0.0287	0.1309	-0.0121	0.0748	50.5603	76.918	19.7518
17	4.7514	-1.0003	-0.2906	6.7772	1.2616	5.4333	0.0721	0.0635	0.0357	-0.1059	0.2501	-0.5278	-0.2307	0.1558	-0.3221	0.118	-0.0095	0.0469	0.1166	-0.054	0.0943	58.6004	68.2539	17.1389
18	5.1958	-1.0597	-1.0756	6.0017	-1.2915	3.9036	-0.0096	0.0691	-0.207	-0.3808	0.0813	-0.0904	0.2781	0.0221	-0.0716	0.1626	-0.0073	0.0307	0.1339	-0.0829	0.0926	56.8387	56.3309	16.0925

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 42
2	X-RAY DIFFRACTION	2	A	43 - 83
3	X-RAY DIFFRACTION	3	A	84 - 125
4	X-RAY DIFFRACTION	4	B	7 - 42
5	X-RAY DIFFRACTION	5	B	43 - 83
6	X-RAY DIFFRACTION	6	B	84 - 125
7	X-RAY DIFFRACTION	7	C	7 - 42
8	X-RAY DIFFRACTION	8	C	43 - 83
9	X-RAY DIFFRACTION	9	C	84 - 125
10	X-RAY DIFFRACTION	10	D	7 - 42
11	X-RAY DIFFRACTION	11	D	43 - 83
12	X-RAY DIFFRACTION	12	D	84 - 125
13	X-RAY DIFFRACTION	13	E	7 - 42
14	X-RAY DIFFRACTION	14	E	43 - 83
15	X-RAY DIFFRACTION	15	E	84 - 125
16	X-RAY DIFFRACTION	16	F	7 - 42
17	X-RAY DIFFRACTION	17	F	43 - 83
18	X-RAY DIFFRACTION	18	F	84 - 125

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