PDB-2ymu: Structure of a highly repetitive propeller structure

ID or keywords:

Entry

Database: PDB / ID: 2ymu

Title

Structure of a highly repetitive propeller structure

Components

WD-40 REPEAT PROTEIN

Keywords

UNKNOWN FUNCTION / TWO DOMAINS

Function / homology

Function and homology information

membrane
Similarity search - Function

Biological species

NOSTOC PUNCTIFORME (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 1.794 Å

Authors

Zeth, K. / Chaudhuri, I. / Martin, J. / Lupas, A.N.

Citation

Journal: To be Published
Title: Structure of a Highly Repetitive Propeller Structure
Authors: Chaudhuri, I. / Zeth, K.

History

Deposition	Oct 10, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2014	Group: Structure summary
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2ymu.cif.gz	446.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2ymu.ent.gz	371.6 KB	Display	PDB format
PDBx/mmJSON format	2ymu.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/ym/2ymu ftp://data.pdbj.org/pub/pdb/validation_reports/ym/2ymu	HTTPS FTP

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Related structure data

Similar structure data	4tzn-d 6u2m-2 1mkx-d 5gkx-d 6l88-1 3js3-2 3kst-d 5dob-d 2ag4-d 3ain-4 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

123 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: WD-40 REPEAT PROTEIN

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

2

B: WD-40 REPEAT PROTEIN

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

Unit cell

Length a, b, c (Å)	88.470, 107.730, 136.260
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	WD-40 REPEAT PROTEIN Mass: 61320.090 Da / Num. of mol.: 2 / Fragment: PROPELLER WITH 14 BLADES, RESIDUES 618-1190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOSTOC PUNCTIFORME (bacteria) / Description: N-TERMINAL HISTAG IN VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B2J0I0
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

WD-40 REPEAT PROTEIN

Mass: 61320.090 Da / Num. of mol.: 2 / Fragment: PROPELLER WITH 14 BLADES, RESIDUES 618-1190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

NOSTOC PUNCTIFORME (bacteria) / Description: N-TERMINAL HISTAG IN VECTOR / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B2J0I0

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 887 / 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: 2.65 Å³/Da / Density % sol: 53.54 % / Description: NONE
Crystal grow	pH: 6.5 / Details: 3.4 M NA MALONATE, pH 6.5

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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
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 121562 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / R_merge(I) obs: 0.13 / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.8→1.91 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 2.05 / % possible all: 92.1

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
SHARP		phasing
DM		phasing
BUCCANEER		phasing

Refinement

Method to determine structure:

MIR
Starting model: NONE

Resolution: 1.794→29.898 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2068	6076	5 %
R_work	0.1739	-	-
obs	0.1755	121562	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.794→29.898 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8646	0	0	887	9533

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	9056
X-RAY DIFFRACTION	f_angle_d	1.423	12396
X-RAY DIFFRACTION	f_dihedral_angle_d	15.162	3234
X-RAY DIFFRACTION	f_chiral_restr	0.1	1426
X-RAY DIFFRACTION	f_plane_restr	0.006	1612

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7935-1.8139	0.3414	185	0.3157	3525	X-RAY DIFFRACTION	92
1.8139-1.8353	0.3191	199	0.2834	3794	X-RAY DIFFRACTION	99
1.8353-1.8576	0.3287	200	0.2706	3795	X-RAY DIFFRACTION	99
1.8576-1.8811	0.3062	200	0.2595	3805	X-RAY DIFFRACTION	100
1.8811-1.9059	0.259	199	0.25	3799	X-RAY DIFFRACTION	99
1.9059-1.932	0.3032	200	0.2341	3819	X-RAY DIFFRACTION	99
1.932-1.9596	0.253	201	0.2178	3817	X-RAY DIFFRACTION	99
1.9596-1.9888	0.2507	202	0.2133	3832	X-RAY DIFFRACTION	100
1.9888-2.0199	0.2503	201	0.2135	3810	X-RAY DIFFRACTION	100
2.0199-2.053	0.2452	202	0.2066	3840	X-RAY DIFFRACTION	100
2.053-2.0884	0.234	200	0.201	3809	X-RAY DIFFRACTION	100
2.0884-2.1264	0.2441	202	0.196	3828	X-RAY DIFFRACTION	100
2.1264-2.1673	0.2334	203	0.1859	3857	X-RAY DIFFRACTION	100
2.1673-2.2115	0.2282	201	0.1847	3824	X-RAY DIFFRACTION	100
2.2115-2.2596	0.1984	202	0.1761	3848	X-RAY DIFFRACTION	100
2.2596-2.3121	0.2141	202	0.176	3830	X-RAY DIFFRACTION	100
2.3121-2.3699	0.2349	200	0.1819	3810	X-RAY DIFFRACTION	100
2.3699-2.4339	0.2313	206	0.1774	3896	X-RAY DIFFRACTION	100
2.4339-2.5055	0.1903	202	0.1702	3855	X-RAY DIFFRACTION	100
2.5055-2.5864	0.2637	203	0.1803	3857	X-RAY DIFFRACTION	100
2.5864-2.6787	0.2325	204	0.1758	3869	X-RAY DIFFRACTION	100
2.6787-2.7859	0.2259	204	0.18	3869	X-RAY DIFFRACTION	100
2.7859-2.9126	0.2135	204	0.1815	3876	X-RAY DIFFRACTION	100
2.9126-3.066	0.1975	203	0.17	3871	X-RAY DIFFRACTION	100
3.066-3.2579	0.1738	206	0.1437	3908	X-RAY DIFFRACTION	100
3.2579-3.5091	0.1714	204	0.1391	3879	X-RAY DIFFRACTION	100
3.5091-3.8616	0.1467	207	0.1289	3936	X-RAY DIFFRACTION	100
3.8616-4.4188	0.1464	207	0.1252	3931	X-RAY DIFFRACTION	100
4.4188-5.5614	0.1351	210	0.1303	3975	X-RAY DIFFRACTION	100
5.5614-29.9025	0.2319	217	0.1962	4122	X-RAY DIFFRACTION	100

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	0.3923	-0.0913	0.0056	0.9658	-0.3192	0.709	-0.0391	0.0183	0.0707	-0.0345	0.0415	0.0123	-0.0979	-0.0391	0.0005	0.1228	-0.0014	-0.0358	0.1319	-0.0036	0.1261	9.4194	-19.7209	-22.0033
2	0.5192	-0.1064	-0.1648	0.7846	-0.201	1.0741	-0.0329	-0.0309	-0.0381	-0.0054	0.0286	0.0304	0.1353	-0.0303	-0.0121	0.0755	0.0101	-0.0001	0.1363	0.0062	0.1168	0.7147	-45.6241	8.6686
3	0.2905	0.1816	-0.089	0.4277	0.1833	0.2082	0.0142	0.0308	-0.0448	-0.1359	-0.0102	-0.0016	-0.0156	0.0287	-0.0224	0.2147	-0.0067	-0.0632	0.1587	-0.0311	0.1748	18.3291	-61.3275	-24.687
4	0.8601	0.2243	-0.2355	0.8578	-0.1282	0.5982	0.0291	0.0527	-0.0532	0.0786	0.0481	0.0174	-0.0659	-0.0261	-0.0317	0.1834	0.0025	-0.0398	0.1448	-0.0151	0.1303	6.9954	-69.1684	-17.1104
5	0.6369	0.0271	-0.3946	1.0111	0.3602	1.0038	0.0775	-0.0494	-0.2309	0.0937	-0.0305	0.1912	0.0525	-0.1433	-0.0093	0.2568	-0.0058	-0.0837	0.1535	0.0098	0.2314	1.796	-88.2444	-18.1329
6	0.8798	-0.0014	-0.0246	1.1005	0.1351	0.6963	0.0045	0.1796	-0.237	-0.0366	0.133	-0.2164	0.0388	0.1769	-0.0421	0.1893	0.0073	-0.0789	0.1735	-0.0611	0.2494	18.3062	-85.5333	-28.6182
7	1.1911	0.5453	-0.0165	0.7814	-0.0134	0.36	0.0451	0.107	-0.1597	-0.027	0.0146	-0.1024	0.1214	0.0613	-0.0529	0.2054	0.0108	-0.0306	0.1892	-0.0413	0.1833	36.0815	-65.1705	-23.7554
8	1.1228	-0.0112	0.6188	1.1373	-0.2107	1.064	0.0713	-0.03	-0.1945	0.0487	0.0516	-0.4739	0.1542	0.2821	-0.0505	0.2122	0.0278	-0.0529	0.2298	-0.0502	0.2867	53.8991	-56.6889	-16.861
9	1.3722	0.1476	0.8818	1.5928	-0.0562	0.8923	0.0394	0.2086	-0.1117	-0.1571	0.0836	-0.4418	0.1477	0.2652	-0.0505	0.2126	-0.0082	-0.0142	0.2268	-0.0164	0.2398	52.8395	-45.1408	-14.7577
10	1.1808	0.1871	0.1041	1.104	0.5532	0.6305	0.0166	0.1009	0.0191	0.0508	0.0026	-0.0755	0.0814	0.0545	-0.0438	0.1254	-0.0162	-0.0061	0.1666	-0.0115	0.1249	40.4745	-38.4599	-15.8594
11	0.6997	-0.0001	0.1157	1.4616	0.3682	0.3229	0.0295	0.0316	0.038	-0.043	-0.0841	0.0187	0.077	0.0624	-0.0335	0.1054	-0.0095	-0.0102	0.1279	-0.0161	0.1183	28.9235	-45.866	-19.6911

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1 THROUGH 281 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 282 THROUGH 577 )
3	X-RAY DIFFRACTION	3	CHAIN B AND (RESID 1 THROUGH 35 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 36 THROUGH 117 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 118 THROUGH 217 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 218 THROUGH 281 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 282 THROUGH 381 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 382 THROUGH 423 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 424 THROUGH 463 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 464 THROUGH 527 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 528 THROUGH 577 )

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