PDB-6xpj: CutR flat hexamer, form 2

ID or keywords:

Entry

Database: PDB / ID: 6xpj

Title

CutR flat hexamer, form 2

Components

Ethanolamine utilization protein EutS

Keywords

STRUCTURAL PROTEIN / microcompartment / MCP / shell protein / BMC

Function / homology

Bacterial microcompartment shell protein EutS/PduU/CutR / bacterial microcompartment / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Bacterial microcompartment shell protein CutR

Function and homology information

Biological species

Streptococcus intermedius SK54 = ATCC 27335 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Ochoa, J.M. / Sawaya, M.R. / Nguyen, V.N. / Duilio, C. / Yeates, T.O.

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2020
Title: Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization.
Authors: Ochoa, J.M. / Nguyen, V.N. / Nie, M. / Sawaya, M.R. / Bobik, T.A. / Yeates, T.O.

History

Deposition	Jul 8, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 11, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3	Oct 18, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6xpj.cif.gz	128.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6xpj.ent.gz	95.5 KB	Display	PDB format
PDBx/mmJSON format	6xpj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6xpj_validation.pdf.gz	453.3 KB	Display	wwPDB validaton report
Full document	6xpj_full_validation.pdf.gz	455.2 KB	Display
Data in XML	6xpj_validation.xml.gz	16.1 KB	Display
Data in CIF	6xpj_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xp/6xpj ftp://data.pdbj.org/pub/pdb/validation_reports/xp/6xpj	HTTPS FTP

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Related structure data

Related structure data	6xphC 6xpiC 6xpkSC 6xplC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ppn-2 6ppn-1 4axi-1 4y15-2 1khx-1 5z1m-d 6p4m-d 6ppp-2 6xpi-d 1u7f-d 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
Related items in Molecule of the Month	#114 - Jun 2009 Vaults similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (4)

Deposited unit

A: Ethanolamine utilization protein EutS

B: Ethanolamine utilization protein EutS

C: Ethanolamine utilization protein EutS

hetero molecules

37.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ethanolamine utilization protein EutS

B: Ethanolamine utilization protein EutS

C: Ethanolamine utilization protein EutS

hetero molecules

A: Ethanolamine utilization protein EutS

B: Ethanolamine utilization protein EutS

C: Ethanolamine utilization protein EutS

hetero molecules

defined by author&software
Evidence: gel filtration, Elutes at molecular weight consistent with hexameric BMC shell proteins.
75 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.290, 79.290, 100.790
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-201- SO4
2	1	C-341- HOH
3	1	C-365- HOH

#1: Protein	Ethanolamine utilization protein EutS Mass: 12377.031 Da / Num. of mol.: 3 / Mutation: K66A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus intermedius SK54 = ATCC 27335 (bacteria) Gene: HMPREF1654_00416 / Plasmid: pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E2IV13
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 2M ammonium sulfate, 0.2M lithium sulfate and 0.1M CAPS/Sodium hydroxide pH 10.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9793 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.5→62.32 Å / Num. obs: 52024 / % possible obs: 99.9 % / Redundancy: 12.954 % / B_iso Wilson estimate: 27.643 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / R_rim(I) all: 0.061 / Χ²: 1.021 / Net I/σ(I): 23.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.5-1.54	12.655	0.855	3.08	3754	0.86	0.891	99.3
1.54-1.58	12.119	0.703	3.73	3709	0.903	0.734	100
1.58-1.63	13.214	0.58	4.67	3581	0.943	0.604	100
1.63-1.68	13.454	0.479	5.82	3490	0.954	0.498	100
1.68-1.73	13.287	0.375	7.27	3408	0.973	0.39	100
1.73-1.79	13.155	0.298	9.16	3260	0.984	0.31	100
1.79-1.86	12.366	0.216	12.02	3192	0.991	0.225	100
1.86-1.94	12.792	0.159	15.93	3060	0.995	0.165	100
1.94-2.02	13.661	0.116	22.38	2923	0.997	0.121	100
2.02-2.12	13.457	0.091	26.81	2819	0.998	0.095	100
2.12-2.24	13.24	0.076	31.25	2695	0.999	0.079	100
2.24-2.37	12.308	0.064	34.59	2542	0.999	0.066	100
2.37-2.54	13.155	0.056	39.89	2405	0.999	0.058	100
2.54-2.74	13.65	0.048	45.93	2252	0.999	0.05	100
2.74-3	13.437	0.042	51.3	2075	0.999	0.043	100
3-3.35	12.576	0.039	55.07	1897	0.999	0.04	100
3.35-3.87	12.474	0.036	59.79	1682	0.999	0.038	100
3.87-4.74	13.157	0.037	64.45	1448	0.999	0.038	99.9
4.74-6.71	11.8	0.039	59.94	1144	0.999	0.041	99.9
6.71-62.32	11.557	0.044	62.09	688	0.999	0.046	99.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	1.5 Å	62.32 Å
Translation	1.5 Å	62.32 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER	2.8.3	phasing
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6XPK

6xpk

Resolution: 1.5→62.318 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.965 / SU B: 2.177 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1841	5203	10.001 %
R_work	0.1607	46821	-
all	0.163	-	-
obs	-	52024	99.919 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.578 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.129 Å²	-0 Å²	0 Å²
2-	-	0.129 Å²	0 Å²
3-	-	-	-0.258 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→62.318 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2486	0	20	200	2706

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	2598
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2438
X-RAY DIFFRACTION	r_angle_refined_deg	1.6	1.624	3553
X-RAY DIFFRACTION	r_angle_other_deg	1.508	1.565	5681
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.244	5	352
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.685	25.321	109
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.807	15	431
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.695	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	383
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2935
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	471
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	486
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	2350
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	1273
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1201
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	131
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.182	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.233	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.112	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	1.598	1.692	1357
X-RAY DIFFRACTION	r_mcbond_other	1.597	1.692	1356
X-RAY DIFFRACTION	r_mcangle_it	2.257	2.536	1695
X-RAY DIFFRACTION	r_mcangle_other	2.256	2.536	1696
X-RAY DIFFRACTION	r_scbond_it	3.393	2.052	1241
X-RAY DIFFRACTION	r_scbond_other	3.158	2.001	1224
X-RAY DIFFRACTION	r_scangle_it	4.88	2.946	1847
X-RAY DIFFRACTION	r_scangle_other	4.639	2.873	1823
X-RAY DIFFRACTION	r_lrange_it	5.466	21.766	2770
X-RAY DIFFRACTION	r_lrange_other	5.366	21.582	2747

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.5-1.539	0.245	375	0.207	3373	0.21	3781	0.907	0.92	99.1272	0.177
1.539-1.581	0.212	370	0.188	3332	0.19	3702	0.93	0.939	100	0.158
1.581-1.627	0.192	359	0.172	3227	0.174	3586	0.944	0.947	100	0.141
1.627-1.677	0.22	349	0.168	3141	0.173	3490	0.936	0.95	100	0.138
1.677-1.732	0.187	340	0.162	3060	0.164	3400	0.952	0.958	100	0.132
1.732-1.793	0.154	327	0.148	2940	0.149	3267	0.97	0.967	100	0.122
1.793-1.86	0.184	318	0.148	2868	0.151	3186	0.959	0.966	100	0.123
1.86-1.936	0.191	306	0.145	2754	0.15	3061	0.959	0.968	99.9673	0.123
1.936-2.022	0.165	293	0.139	2633	0.141	2926	0.971	0.975	100	0.122
2.022-2.121	0.166	282	0.147	2542	0.149	2824	0.97	0.973	100	0.133
2.121-2.235	0.192	269	0.152	2417	0.156	2686	0.96	0.967	100	0.14
2.235-2.371	0.17	254	0.148	2292	0.15	2546	0.968	0.971	100	0.14
2.371-2.534	0.171	240	0.148	2155	0.15	2395	0.969	0.971	100	0.144
2.534-2.737	0.18	226	0.153	2033	0.155	2259	0.962	0.971	100	0.155
2.737-2.997	0.179	206	0.159	1861	0.161	2068	0.965	0.968	99.9516	0.166
2.997-3.35	0.192	191	0.16	1711	0.163	1902	0.958	0.967	100	0.177
3.35-3.867	0.177	168	0.164	1514	0.166	1682	0.964	0.967	100	0.187
3.867-4.731	0.167	145	0.152	1306	0.154	1452	0.975	0.975	99.9311	0.185
4.731-6.672	0.229	115	0.211	1033	0.213	1149	0.96	0.965	99.913	0.259
6.672-62.318	0.198	70	0.189	629	0.19	704	0.967	0.972	99.2898	0.268

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	0.2189	-0.1664	-0.0253	0.2709	-0.1767	0.2737	-0.0477	-0.0509	0.0012	0.0265	0.0473	0.0012	0.026	0.0031	0.0004	0.0312	0.0113	0.005	0.0301	-0.002	0.0109	10.196	15.424	19.828
2	0.0329	-0.0074	-0.0647	0.3534	-0.0097	0.1372	-0.0018	-0.0044	0.0079	0.0057	0.0195	0.0102	0.0191	0.0134	-0.0177	0.0284	0.0076	-0.006	0.0275	0.0146	0.0177	23.685	2.477	12.944
3	0.0492	-0.0141	0.0753	0.0672	0.0792	0.2829	0.0291	0.0275	0.0041	-0.0133	-0.0441	-0.0008	0.03	-0.0127	0.015	0.0248	0.0157	-0.0006	0.0379	0.0037	0.0272	25.652	2.287	-5.075

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	9 - 116
2	X-RAY DIFFRACTION	2	ALL	BBB	8 - 116
3	X-RAY DIFFRACTION	3	ALL	CCC	0 - 116

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