PDB-5idr: Crystal structure of Proteus Mirabilis ScsC in a transitional con...

ID or keywords:

Entry

Database: PDB / ID: 5idr

Title

Crystal structure of Proteus Mirabilis ScsC in a transitional conformation

Components

DsbA-like protein

Keywords

ISOMERASE / thioredoxin fold / disulfide isomerase / trimer / copper resistance

Function / homology

:

Function and homology information

Biological species

Proteus mirabilis ATCC 29906 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.562 Å

Authors

Furlong, E.J. / Kurth, F. / Choudhury, H.G. / Martin, J.L.

Funding support

Australia, 1items

Citation

Journal: Nat Commun / Year: 2017
Title: A shape-shifting redox foldase contributes to Proteus mirabilis copper resistance.
Authors: Furlong, E.J. / Lo, A.W. / Kurth, F. / Premkumar, L. / Totsika, M. / Achard, M.E.S. / Halili, M.A. / Heras, B. / Whitten, A.E. / Choudhury, H.G. / Schembri, M.A. / Martin, J.L.

History

Deposition	Feb 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2018	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 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	5idr.cif.gz	733.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5idr.ent.gz	627.2 KB	Display	PDB format
PDBx/mmJSON format	5idr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5idr_validation.pdf.gz	463.6 KB	Display	wwPDB validaton report
Full document	5idr_full_validation.pdf.gz	469.4 KB	Display
Data in XML	5idr_validation.xml.gz	42.9 KB	Display
Data in CIF	5idr_validation.cif.gz	59.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/id/5idr ftp://data.pdbj.org/pub/pdb/validation_reports/id/5idr	HTTPS FTP

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Related structure data

Related structure data	4xvwC 4yx8 PDB Unreleased entryS 5id4 6nen S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6pe9-2 7k0x-1 5j7r-3 4i18-2 1yew-1 6yxq-d 4ehp-d 3f7p-2 1qun-7 5iw7-1 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DsbA-like protein

B: DsbA-like protein

C: DsbA-like protein

D: DsbA-like protein

E: DsbA-like protein

F: DsbA-like protein

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

1

A: DsbA-like protein

B: DsbA-like protein

C: DsbA-like protein

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

2

D: DsbA-like protein

E: DsbA-like protein

F: DsbA-like protein

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

Unit cell

Length a, b, c (Å)	193.054, 193.054, 105.806
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

#1: Protein	DsbA-like protein Mass: 24800.443 Da / Num. of mol.: 6 / Fragment: UNP residues 22-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis ATCC 29906 (bacteria) Gene: HMPREF0693_3732 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C2LPE2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

DsbA-like protein

Mass: 24800.443 Da / Num. of mol.: 6 / Fragment: UNP residues 22-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Proteus mirabilis ATCC 29906 (bacteria)
Gene: HMPREF0693_3732 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C2LPE2

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.31 Å³/Da / Density % sol: 63 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 2.85 M Sodium malonate pH 5.8, 0.1 M Copper(II) chloride

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX2 / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.56→42.817 Å / Num. obs: 62124 / % possible obs: 99.4 % / Redundancy: 4.1 % / B_iso Wilson estimate: 44.4 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.083 / R_pim(I) all: 0.047 / R_rim(I) all: 0.096 / Net I/σ(I): 14.9 / Num. measured all: 254817

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.56-2.7	4.1	0.725	36519	8979	0.703	0.415	0.837	2.4	99.3
8.1-136.51	3.9	0.023	7933	2015	0.998	0.013	0.027	50.5	98.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
Aimless	0.5.8	data scaling
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YX8

4yx8
PDB Unreleased entry

Resolution: 2.562→42.817 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2216	3011	4.85 %
R_work	0.1709	59058	-
obs	0.1734	62069	99.32 %

Solvent computation

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

Displacement parameters

B_iso max: 151.2 Å² / B_iso mean: 55.4858 Å² / B_iso min: 14.47 Å²

Refinement step

Cycle: final / Resolution: 2.562→42.817 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10190	0	0	82	10272
B_iso mean	-	-	-	42.96	-
Num. residues	-	-	-	-	1315

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10414
X-RAY DIFFRACTION	f_angle_d	1.047	14102
X-RAY DIFFRACTION	f_chiral_restr	0.038	1675
X-RAY DIFFRACTION	f_plane_restr	0.005	1831
X-RAY DIFFRACTION	f_dihedral_angle_d	13.281	4002

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.562-2.6018	0.3107	117	0.2742	2666	2783	100
2.6018-2.6445	0.3073	123	0.2747	2712	2835	100
2.6445-2.6901	0.3904	148	0.2698	2592	2740	98
2.6901-2.739	0.3262	134	0.268	2681	2815	100
2.739-2.7917	0.3096	136	0.2375	2731	2867	100
2.7917-2.8486	0.3136	153	0.2422	2638	2791	100
2.8486-2.9106	0.2687	113	0.2297	2714	2827	100
2.9106-2.9783	0.2685	152	0.223	2711	2863	100
2.9783-3.0527	0.3182	139	0.2173	2654	2793	100
3.0527-3.1352	0.3103	116	0.202	2719	2835	100
3.1352-3.2275	0.2211	144	0.2055	2706	2850	100
3.2275-3.3316	0.2503	146	0.1832	2693	2839	100
3.3316-3.4506	0.2588	132	0.1864	2586	2718	97
3.4506-3.5887	0.2044	128	0.1711	2705	2833	100
3.5887-3.752	0.2085	130	0.1536	2653	2783	98
3.752-3.9496	0.1959	135	0.1453	2599	2734	97
3.9496-4.1969	0.1791	157	0.1292	2705	2862	100
4.1969-4.5206	0.1649	133	0.1168	2669	2802	100
4.5206-4.9749	0.1864	136	0.1272	2730	2866	100
4.9749-5.6934	0.201	132	0.1464	2727	2859	100
5.6934-7.1676	0.1955	133	0.1614	2753	2886	100
7.1676-42.8232	0.1647	174	0.1411	2714	2888	99

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	0.2334	0.0072	-0.0016	0.2589	-0.1489	-0.0582	0.0475	0.0346	-0.0129	-0.0052	-0.0756	-0.1702	-0.0342	0.0917	-0	0.3313	0.0403	0.0799	0.2891	0.0005	0.3592	54.8431	-16.452	82.2719
2	0.285	0.2565	0.2926	0.486	0.1012	0.5142	-0.0567	-0.0322	-0.1548	-0.0262	0.0322	-0.0309	0.0155	0.008	-0	0.2375	0.0526	0.0056	0.1917	-0.0026	0.2807	38.3035	-38.4367	93.8724
3	0.3782	-0.1952	-0.0407	0.8105	0.6642	0.8553	0.0655	-0.0466	-0.0173	-0.0249	-0.002	-0.0915	-0.2292	-0.0529	-0	0.3136	0.0405	0.0113	0.2352	0.0224	0.3164	41.467	-33.9816	95.4019
4	0.1342	0.0741	0.2185	0.1559	0.1704	0.3475	0.3492	0.4084	0.1804	0.0242	-0.2866	-0.0502	-0.0763	0.1459	-0.0002	0.521	0.036	0.0572	0.6139	0.0376	0.4806	63.053	4.0068	70.8353
5	0.2497	0.2892	0.153	0.2498	0.0606	0.1641	-0.0306	-0.0587	-0.2246	0.0945	-0.051	0.1981	0.1805	-0.1193	-0.0001	0.3513	-0.0372	0.0234	0.1406	-0.0119	0.353	39.444	-11.5444	81.7553
6	0.8039	-0.2156	-0.5688	1.1933	0.1877	1.1945	0.0011	0.1084	0.0306	-0.0963	-0.0473	0.0174	0.0458	-0.2278	-0	0.2944	-0.0602	0.0009	0.2661	0.0111	0.2865	30.3628	-0.0502	81.1688
7	0.2457	0.229	0.0887	0.2409	0.1436	0.0694	-0.114	0.0905	-0.2368	-0.1887	0.0698	0.1611	0.0467	0.2385	-0.0001	0.5003	0.042	0.1059	0.4624	-0.0278	0.4668	61.4318	2.0268	72.4673
8	0.3905	-0.2392	-0.1774	0.7645	-0.364	1.0371	0.0927	0.1711	-0.0185	-0.2073	-0.0458	-0.178	-0.0127	-0.2748	0	0.311	-0.0727	0.0363	0.3256	0.0301	0.2706	36.939	20.4827	61.7548
9	0.202	-0.1126	0.0703	0.4338	-0.2282	1.9132	0.1354	0.0511	-0.0697	-0.1354	-0.0579	-0.0207	0.2528	-0.2694	0.0291	0.2007	-0.0067	0.0468	0.1794	0.004	0.1152	37.7437	16.4436	58.7561
10	0.1861	0.06	0.1081	0.1485	-0.0365	0.0517	-0.044	0.2961	-0.2096	0.1421	0.1607	-0.2325	0.2568	-0.3923	-0.0002	0.2455	0.0008	-0.0341	0.2213	0.023	0.329	52.6203	-45.8239	128.5133
11	0.2509	0.0242	0.1422	0.2223	-0.1289	0.2417	-0.0626	0.1276	0.0633	-0.0873	0.0734	-0.0458	0.1617	-0.0148	0	0.354	0.0597	-0.0229	0.2797	0.0325	0.3543	54.0075	-17.3257	111.3417
12	0.7166	0.2028	-0.1946	1.2056	-0.0403	1.2583	0.0454	0.0056	0.0076	0.1282	-0.0328	-0.2035	-0.0161	0.0898	0	0.2708	-0.0032	-0.0192	0.2165	0.0384	0.3257	54.0863	7.2992	100.6441
13	0.2154	0.2583	0.0189	0.5061	-0.2066	0.4371	0.1532	-0.4196	-0.1264	-0.3787	0.0675	-0.0594	-0.0423	-0.324	-0.0001	0.3027	0.0158	-0.0253	0.3404	0.0019	0.3211	49.639	-38.1025	124.417
14	0.7421	-0.0472	0.2086	0.5846	0.3287	1.9799	-0.2176	-0.0103	0.635	0.147	-0.0605	-0.0734	-0.2934	-0.5529	-0.0528	0.5114	-0.044	-0.0569	-0.0146	-0.0395	0.3246	38.5261	-12.141	112.9822
15	0.9078	0.1628	0.4708	0.8776	-0.5326	1.2432	-0.0707	-0.2158	0.0356	0.1093	-0.0504	0.0454	-0.2428	-0.2707	-0.0004	0.3831	0.1079	-0.0083	0.2557	-0.0556	0.2625	24.9918	-16.5225	113.5243
16	0.3749	-0.0464	-0.3086	0.4579	-0.0118	0.4259	0.1314	-0.0445	0.1013	0.108	-0.0901	0.0149	0.0946	-0.0096	0	0.3018	0.0022	-0.014	0.1928	-0.0098	0.2806	42.3476	-38.8117	123.2457
17	0.21	0.4579	-0.3047	0.1473	-0.2191	1.7034	0.0796	-0.2792	0.0333	-0.0447	-0.0364	-0.0159	-0.3168	-0.2563	0.0007	0.2793	0.0877	-0.0031	0.4476	0.0012	0.2644	20.1747	-35.0576	135.7199

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 85 )	A	4 - 85
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 86 through 147 )	A	86 - 147
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 148 through 222 )	A	148 - 222
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 37 )	B	4 - 37
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 38 through 64 )	B	38 - 64
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 65 through 222 )	B	65 - 222
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 5 through 42 )	C	5 - 42
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 43 through 123 )	C	43 - 123
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 124 through 222 )	C	124 - 222
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 2 through 20 )	D	2 - 20
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 21 through 62 )	D	21 - 62
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 63 through 222 )	D	63 - 222
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 3 through 37 )	E	3 - 37
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 38 through 65 )	E	38 - 65
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 66 through 223 )	E	66 - 223
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 1 through 59 )	F	1 - 59
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 60 through 222 )	F	60 - 222

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