PDB-6xph: CutR dimer with domain swap

ID or keywords:

Entry

Database: PDB / ID: 6xph

Title

CutR dimer with domain swap

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 / : / THIOCYANATE ION / 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: 1.8 Å

Authors

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

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 / Derived calculations Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2	Oct 14, 2020	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3	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 1.4	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
Revision 1.5	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6xph.cif.gz	89.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6xph_validation.pdf.gz	427.8 KB	Display	wwPDB validaton report
Full document	6xph_full_validation.pdf.gz	427.8 KB	Display
Data in XML	6xph_validation.xml.gz	6.2 KB	Display
Data in CIF	6xph_validation.cif.gz	9.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xp/6xph ftp://data.pdbj.org/pub/pdb/validation_reports/xp/6xph	HTTPS FTP

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Related structure data

Related structure data	6xpiC 6xpjC 6xpkC 6xplC 4axiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4oyj-10 2f4i-1 5hx4-1 2v0v-4 3pvp-2 3mlf-1 5bnd-1 5iqy-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	#114 - Jun 2009 Vaults similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (4) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Ethanolamine utilization protein EutS

B: Ethanolamine utilization protein EutS

hetero molecules

27 kDa, 2 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)	110.290, 110.290, 110.290
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	212
Space group name H-M	P4₃32

Components on special symmetry positions

ID	Model	Components
1	1	B-339- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Ethanolamine utilization protein EutS Mass: 13324.064 Da / Num. of mol.: 2 / Mutation: K66D 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

#1: Protein

Ethanolamine utilization protein EutS

Mass: 13324.064 Da / Num. of mol.: 2 / Mutation: K66D
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

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Non-polymers , 5 types, 135 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.1 Å³/Da / Density % sol: 41.36 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Potassium thiocyanate, 30% w/v PEG 2000

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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: 0.9792 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 1.8→77.541 Å / Num. obs: 21478 / % possible obs: 100 % / Redundancy: 75.744 % / B_iso Wilson estimate: 36.863 Å² / CC_1/2: 1 / R_merge(I) obs: 0.079 / R_rim(I) all: 0.079 / Χ²: 0.891 / Net I/σ(I): 49.24

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
1.8-1.85	75.197	1.391	4.71	1557	0.949	1.401	100
1.85-1.9	80.855	1.045	6.66	1497	0.973	1.051	100
1.9-1.95	80.293	0.769	9.19	1469	0.984	0.774	100
1.95-2.01	79.221	0.517	13.88	1434	0.993	0.52	100
2.01-2.08	78.29	0.388	18.21	1393	0.996	0.391	100
2.08-2.15	74.639	0.32	21.42	1351	0.997	0.322	100
2.15-2.23	73.922	0.246	27.47	1296	0.998	0.248	100
2.23-2.32	81.031	0.207	33.64	1250	0.999	0.208	99.4
2.32-2.43	80.153	0.173	39.39	1232	0.999	0.174	100
2.43-2.55	78.88	0.14	46.94	1145	0.999	0.141	100
2.55-2.68	76.387	0.119	53.72	1110	0.999	0.12	100
2.68-2.85	69.743	0.09	66.91	1046	1	0.091	99.9
2.85-3.04	78.725	0.073	85.54	1004	1	0.073	100
3.04-3.29	76.203	0.06	97.56	923	1	0.06	100
3.29-3.6	73.282	0.049	113.75	868	1	0.049	100
3.6-4.03	67	0.044	120.45	784	1	0.044	100
4.03-4.65	67.951	0.037	133.44	712	1	0.037	100
4.65-5.69	69.761	0.037	129.57	606	1	0.038	99.8
5.69-8.05	59.439	0.039	120.81	492	1	0.04	100
8.05-77.541	58.1	0.03	132.89	309	1	0.03	100

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.8 Å	45.03 Å
Translation	2.8 Å	45.03 Å

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4AXI

4axi

Resolution: 1.8→77.541 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.955 / WR_factor R_free: 0.203 / WR_factor R_work: 0.171 / SU B: 4.553 / SU ML: 0.074 / Average fsc free: 0.943 / Average fsc work: 0.9545 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2102	2149	10.002 %
R_work	0.1757	19336	-
all	0.179	-	-
obs	-	21478	100 %

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: 33.354 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.8→77.541 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1462	0	21	128	1611

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	1554
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	1456
X-RAY DIFFRACTION	r_angle_refined_deg	1.84	1.624	2130
X-RAY DIFFRACTION	r_angle_other_deg	2.395	1.565	3394
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.178	5	216
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.295	25.806	62
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.251	15	248
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.122	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	233
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	1762
X-RAY DIFFRACTION	r_gen_planes_other	0.023	0.02	284
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	317
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	1336
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	782
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	686
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	100
X-RAY DIFFRACTION	r_metal_ion_refined	0.261	0.2	14
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.126	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.112	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	2.667	2.831	812
X-RAY DIFFRACTION	r_mcbond_other	2.582	2.821	809
X-RAY DIFFRACTION	r_mcangle_it	3.43	4.221	1014
X-RAY DIFFRACTION	r_mcangle_other	3.457	4.222	1015
X-RAY DIFFRACTION	r_scbond_it	5.439	3.37	742
X-RAY DIFFRACTION	r_scbond_other	5.43	3.365	741
X-RAY DIFFRACTION	r_scangle_it	7.587	4.831	1106
X-RAY DIFFRACTION	r_scangle_other	7.562	4.828	1105
X-RAY DIFFRACTION	r_lrange_it	7.86	36.941	1726
X-RAY DIFFRACTION	r_lrange_other	7.882	36.954	1727

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

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	WR_factor R_work
1.8-1.847	0.273	154	0.237	1386	0.24	1540	0.918	0.933	0.191
1.847-1.897	0.249	152	0.21	1365	0.214	1517	0.925	0.938	0.168
1.897-1.952	0.264	145	0.205	1308	0.211	1453	0.921	0.936	0.166
1.952-2.012	0.255	144	0.175	1295	0.183	1439	0.922	0.951	0.148
2.012-2.078	0.208	141	0.169	1263	0.173	1404	0.948	0.958	0.142
2.078-2.151	0.215	134	0.172	1213	0.176	1347	0.951	0.959	0.145
2.151-2.232	0.213	130	0.17	1163	0.174	1293	0.948	0.96	0.145
2.232-2.323	0.215	125	0.164	1130	0.169	1255	0.944	0.964	0.14
2.323-2.427	0.22	122	0.167	1093	0.172	1215	0.949	0.956	0.138
2.427-2.545	0.237	116	0.17	1049	0.176	1165	0.939	0.959	0.144
2.545-2.682	0.21	111	0.179	994	0.182	1105	0.951	0.956	0.158
2.682-2.845	0.225	104	0.188	940	0.192	1044	0.94	0.948	0.17
2.845-3.041	0.228	100	0.187	903	0.191	1003	0.945	0.953	0.176
3.041-3.284	0.2	93	0.188	834	0.189	927	0.957	0.958	0.18
3.284-3.597	0.232	86	0.184	777	0.189	863	0.955	0.962	0.184
3.597-4.021	0.197	80	0.156	715	0.16	795	0.962	0.968	0.165
4.021-4.64	0.19	70	0.143	631	0.148	701	0.969	0.977	0.157
4.64-5.678	0.156	61	0.178	554	0.176	615	0.973	0.972	0.198
5.678-8.009	0.165	49	0.199	440	0.195	489	0.973	0.965	0.22
8.009-77.541	0.238	32	0.171	282	0.177	314	0.95	0.979	0.221

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	0.9414	-0.2489	-0.4306	0.3093	0.0802	0.2619	0.0348	0.0418	-0.0284	0.0728	-0.0279	0.057	0.0108	-0.0607	-0.0069	0.0629	-0.0247	-0.0005	0.0402	-0.0014	0.0204	-34.818	8.935	1.648
2	0.7587	0.421	-0.1157	0.4952	-0.1733	0.2531	0.0386	0.0205	-0.0353	-0.0161	-0.0462	-0.0315	0.0007	0.073	0.0077	0.0437	0.0078	-0.001	0.0327	0.0035	0.0144	-17.923	9.956	0.448

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	18 - 116
2	X-RAY DIFFRACTION	2	ALL	BBB	18 - 116

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