PDB-4axj: Structure of the Clostridium difficile EutM protein

ID or keywords:

Entry

Database: PDB / ID: 4axj

Title

Structure of the Clostridium difficile EutM protein

Components

ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

Keywords

STRUCTURAL PROTEIN / ETHANOLAMINE / BACTERIAL MICROCOMPARTMENT / BMC

Function / homology

Function and homology information

ethanolamine catabolic process / bacterial microcompartment
Similarity search - Function

Biological species

CLOSTRIDIUM DIFFICILE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.62 Å

Authors

Pitts, A.C. / Tuck, L.R. / Faulds-Pain, A. / Lewis, R.J. / Marles-Wright, J.

Citation

Journal: Plos One / Year: 2012
Title: Structural Insight Into the Clostridium Difficile Ethanolamine Utilisation Microcompartment.
Authors: Pitts, A.C. / Tuck, L.R. / Faulds-Pain, A. / Lewis, R.J. / Marles-Wright, J.

History

Deposition	Jun 13, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 20, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 11, 2012	Group: Other
Revision 1.2	Jan 9, 2013	Group: Database references
Revision 1.3	May 8, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4axj.cif.gz	145.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4axj.ent.gz	118.6 KB	Display	PDB format
PDBx/mmJSON format	4axj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4axj_validation.pdf.gz	440.5 KB	Display	wwPDB validaton report
Full document	4axj_full_validation.pdf.gz	442.5 KB	Display
Data in XML	4axj_validation.xml.gz	13.9 KB	Display
Data in CIF	4axj_validation.cif.gz	19.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ax/4axj ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4axj	HTTPS FTP

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Related structure data

Related structure data	4axiC 4axoC 2ewhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4rbv-2 4p2s-2 5l38-1 4qig-1 4qie-1 4qig-3 4p7v-d 4qie-2 4p7t-d 4qig-2 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 (7) #165 - Sep 2013 Designed Protein Cages similarity (4)

Deposited unit

A: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

B: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

C: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

hetero molecules

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

1

A: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

B: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

C: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

hetero molecules

A: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

B: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

C: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN

hetero molecules

defined by author&software
64.1 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.368, 46.380, 76.400
Angle α, β, γ (deg.)	90.00, 91.56, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	A-1092- SO4

#1: Protein	ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN / EUTM Mass: 10626.194 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: 630 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q187N0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	INSERTION OF GLYCINE AT N-TERMINUS AFTER INITIATING METHIONINE AND C-TERMINAL HIS-TAG.

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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: 43.22 % / Description: NONE
Crystal grow	Method: vapor diffusion, sitting drop / pH: 4.2 Details: PROTEIN IN H2O AT 10 MG/ML. CRYSTALLISED BY SITTING DROP VAPOUR DIFFUSION, 100/100 NL DROPS, 100 UL WELL. WELL SOLUTION OF 200 MM LI2SO4, 100 MM PHOSPHATE/CITRATE PH 4.2, 20 % W/V PEG 1000.

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9804
Detector	Type: ADSC CCD / Detector: CCD / Date: Jan 25, 2010 / Details: MIRRORS
Radiation	Monochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9804 Å / Relative weight: 1
Reflection	Resolution: 1.62→38.2 Å / Num. obs: 30458 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / B_iso Wilson estimate: 17 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shell	Resolution: 1.62→1.71 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 3.5 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EWH

2ewh

Resolution: 1.62→23.691 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 18.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1959	1527	5 %
R_work	0.1646	-	-
obs	0.1662	30452	98.01 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.918 Å² / k_sol: 0.391 e/Å³

Displacement parameters

B_iso mean: 15.88 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.334 Å²	0 Å²	-0.7064 Å²
2-	-	12.6948 Å²	0 Å²
3-	-	-	5.9833 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→23.691 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1827	0	10	206	2043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	1872
X-RAY DIFFRACTION	f_angle_d	1.547	2546
X-RAY DIFFRACTION	f_dihedral_angle_d	12.797	666
X-RAY DIFFRACTION	f_chiral_restr	0.113	318
X-RAY DIFFRACTION	f_plane_restr	0.008	334

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 (%)
1.62-1.6779	0.2571	161	0.2207	2866	X-RAY DIFFRACTION	98
1.6779-1.7451	0.2281	142	0.1976	2865	X-RAY DIFFRACTION	98
1.7451-1.8244	0.2202	151	0.1707	2853	X-RAY DIFFRACTION	98
1.8244-1.9206	0.1838	136	0.1591	2922	X-RAY DIFFRACTION	98
1.9206-2.0409	0.2352	131	0.1585	2907	X-RAY DIFFRACTION	98
2.0409-2.1983	0.194	159	0.1591	2906	X-RAY DIFFRACTION	99
2.1983-2.4194	0.1979	162	0.1509	2893	X-RAY DIFFRACTION	99
2.4194-2.769	0.1999	157	0.1543	2925	X-RAY DIFFRACTION	99
2.769-3.4869	0.1989	155	0.1705	2945	X-RAY DIFFRACTION	99
3.4869-23.6931	0.1727	173	0.1627	2843	X-RAY DIFFRACTION	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	0.0218	-0.0116	-0.0304	0.0338	0.0392	0.0643	0.0057	0.0055	-0.0113	0.0007	0.0083	-0.0073	0.0277	0.0216	0.1557	-0.0207	0.0379	-0.0366	0.026	0.0066	-0.0153	-18.0801	13.2141	-13.7668
2	0.0023	-0.0043	0.0023	0.0106	-0.0072	0.0096	0.0363	0.0337	-0.0122	-0.0093	0.0022	0.0117	0.0239	0.0411	0.0668	0.0741	0.046	-0.0101	0.0622	-0.0198	0.0818	-17.0032	7.0539	-11.9016
3	0.0122	-0.0007	-0.0013	0.006	-0.0039	0.0044	0.0039	-0.0082	-0.0109	0.0073	0.0135	-0.0201	0.0274	0.0232	0.0884	0.0012	0.0481	-0.0346	0.0443	-0.0168	0.0131	-18.5108	11.5102	-7.784
4	0.0118	0.0033	-0.0056	0.0193	-0.0094	0.0154	0.0079	0.0087	0.0226	0.001	0.0108	0.0224	-0.0189	0.0158	0.1462	0.0162	-0.0298	0.0224	0.0635	0.0566	0.0422	-13.1632	18.2148	-15.8593
5	0.0096	0.0055	-0.0114	0.0034	-0.0052	0.0198	0.0112	0.0028	-0.0082	0.0064	-0.0018	-0.0094	-0.0066	-0.009	0.0832	0.0221	0.0376	-0.0206	0.0459	0.0046	0.0259	-16.5666	19.7103	-7.7779
6	0.021	0.013	-0.028	0.0106	-0.0105	0.0689	-0.0103	0.0254	-0.0001	0.0062	0.0164	-0.0106	0.0421	0.0361	-0.0015	0.059	0.0272	-0.0156	0.0622	-0.0071	0.0185	-9.7628	5.8008	0.2587
7	0.0067	0.0028	0.0032	0.0026	-0.0007	0.0041	0.009	-0.0066	-0.0036	-0.0005	-0.0053	-0.0037	0.0076	0.0037	-0.001	0.0133	0.0313	-0.0074	0.0115	-0.041	0.025	-30.5351	12.1267	-21.2551
8	0.0051	0.0059	0	0.0067	0.0007	0.0003	0.0072	-0.0066	-0.0318	-0.0113	0.002	0.0024	0.0084	0.0045	0.0778	-0.0092	-0.023	-0.0193	-0.033	-0.0432	0.0246	-37.984	10.7768	-20.3568
9	0.0021	0.0039	-0.0028	0.0102	-0.0082	0.0063	0.0067	-0.0001	0.0113	0.0166	0.0074	0.0134	-0.0212	-0.0114	0.1345	0.0261	0.0388	0.0073	-0.0026	0.0134	0.0002	-37.4808	18.155	-26.9116
10	0.0014	0.0034	0.0051	0.0188	0.0176	0.0189	0.0305	-0.008	-0.0014	0.0004	0.0066	-0.0136	0.0106	0.0089	0.4335	0.0427	0.0466	0.0142	-0.0049	-0.0438	0.0338	-26.1739	11.2151	-21.6794
11	0.0302	-0.0034	0.0303	0.0177	-0.0021	0.0319	0.0017	0.0012	-0.0104	-0.0054	0.0046	-0.0002	0.0053	0.0036	0.0194	0.0143	-0.0248	0.0002	0.0229	-0.0192	0.0149	-50.8259	14.6313	-11.4792
12	0.0026	-0.003	0.0006	0.0039	-0.0017	0.0033	0.0011	0.0069	0.0052	-0.0087	0.0136	0.0097	0.0018	-0.0132	0.1661	-0.0126	-0.0203	0.0087	0.0118	0.0165	0.0048	-58.1615	13.2918	-3.9005
13	0.0116	-0.0042	0.0018	0.0105	-0.0043	0.0024	-0.0088	0.0047	-0.006	0.0027	-0.0021	-0.0032	0.0145	-0.0058	-0.0747	0.0375	-0.0214	-0.0318	0.0225	-0.0292	0.0455	-54.2763	7.4387	-9.4507
14	0.1433	0.0017	0.0998	0.198	0.1094	0.1329	-0.0038	0.0045	-0.0099	-0.0186	-0.0018	0.027	0.0074	-0.0051	-0.0007	0.005	-0.0516	-0.0297	0.0581	-0.0097	0.0012	-49.8361	11.7881	-10.4275
15	0.1409	-0.0851	-0.0738	0.052	0.0482	0.0834	0.0322	0.0003	0.0507	0.026	0.0433	0.0424	-0.0818	-0.0497	0.0644	0.0536	-0.0026	0.0137	0.0326	0.0131	0.0346	-59.5808	18.9322	-10.373
16	0.0026	0.0049	0.0024	0.0197	0.0096	0.0092	0.0105	-0.0139	0.0063	0.0141	-0.0082	-0.007	-0.0079	0.0054	-0.0129	0.0563	-0.0422	0.0229	0.0245	-0.0108	0.0397	-50.9009	20.3643	-11.5288
17	0.0071	-0.0056	0.0052	0.0043	-0.0041	0.0041	-0.0171	0.0271	-0.0401	-0.0064	0.0053	-0.0414	0.003	-0.0071	-0.0354	0.1361	-0.0515	0.0282	0.0727	-0.0393	0.116	-47.4565	6.3093	-21.7753

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 4:28)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 29:38)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 39:51)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 52:69)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 70:78)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 79:90)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 2:14)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 15:51)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 52:69)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 70:90)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESSEQ 5:14)
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESSEQ 15:28)
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESSEQ 29:38)
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 39:51)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 52:69)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 70:78)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 79:90)

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