PDB-7s1d: Crystal structure of E.coli DsbA in complex with compound MIPS-00...

ID or keywords:

Entry

Database: PDB / ID: 7s1d

Title

Crystal structure of E.coli DsbA in complex with compound MIPS-0001877 (compound 39)

Components

Thiol:disulfide interchange protein DsbA

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / thioredoxin fold / thiol-disulfide oxidoreductase / inhibitor / DsbA / oxidoreductase-inhibitor complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex

Function / homology

Function and homology information

cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.59 Å

Authors

Heras, B. / Scanlon, M.J. / Martin, J.L. / Caria, S.

Funding support

Australia, 1items

Citation

Journal: Chemrxiv / Year: 2022
Title: Fluoromethylketone-fragment conjugates designed as covalent modifiers of EcDsbA are atypical substrates
Authors: Bradley, C.D. / Whitehouse, R.L. / Rimmer, K. / Williams, M. / Heras, B. / Caria, S. / Ilyichova, O. / Vazirani, M. / Mohanty, B. / Harper, J. / Scanlon, M.J. / Simpson, J.S.

History

Deposition	Sep 2, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Oct 23, 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	7s1d.cif.gz	175.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7s1d.ent.gz	138.8 KB	Display	PDB format
PDBx/mmJSON format	7s1d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7s1d_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	7s1d_full_validation.pdf.gz	2.2 MB	Display
Data in XML	7s1d_validation.xml.gz	21.7 KB	Display
Data in CIF	7s1d_validation.cif.gz	32.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s1/7s1d ftp://data.pdbj.org/pub/pdb/validation_reports/s1/7s1d	HTTPS FTP

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Related structure data

Related structure data	7s1cC 7s1fC 7s1lC C: citing same article (ref.)
Similar structure data	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	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (2) #91 - Jul 2007 Thymine Dimers similarity (2)

Deposited unit

A: Thiol:disulfide interchange protein DsbA

B: Thiol:disulfide interchange protein DsbA

hetero molecules

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

1

A: Thiol:disulfide interchange protein DsbA

hetero molecules

defined by author&software
Evidence: gel filtration
21.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Thiol:disulfide interchange protein DsbA

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.966, 64.220, 74.356
Angle α, β, γ (deg.)	90.000, 126.040, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-467- HOH

#1: Protein	Thiol:disulfide interchange protein DsbA Mass: 21155.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0AEG4
#2: Chemical	ChemComp-648 / 1-[3-(thiophen-3-yl)benzyl]piperidin-2-one Mass: 271.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₁₇NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.65 Å³/Da / Density % sol: 53.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 11-13% PEG 8000, 5-7.5% glycerol, 1 mM CuCl2, 100 mM sodium cacodylate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX1 / Wavelength: 0.95369 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2011

Radiation

Monochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.95369 Å / Relative weight: 1

Reflection

Resolution: 1.59→56.423 Å / Num. all: 58965 / Num. obs: 58965 / % possible obs: 99.3 % / Redundancy: 3.9 % / B_iso Wilson estimate: 18.33 Å² / R_pim(I) all: 0.022 / R_rim(I) all: 0.044 / R_sym value: 0.038 / Net I/av σ(I): 15.048 / Net I/σ(I): 20 / Num. measured all: 232207

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_pim(I) all	R_sym value	% possible all
1.59-1.68	4	0.402	2	8519	0.232	0.402	98.9
1.68-1.78	4	0.27	2.9	8117	0.155	0.27	99.1
1.78-1.9	4	0.161	4.9	7644	0.093	0.161	99.3
1.9-2.05	4	0.095	8.3	7117	0.055	0.095	99.5
2.05-2.25	3.9	0.059	13	6566	0.034	0.059	99.6
2.25-2.51	3.9	0.043	17.7	5940	0.025	0.043	99.6
2.51-2.9	3.9	0.032	22.8	5266	0.018	0.032	99.6
2.9-3.56	3.9	0.023	29	4443	0.013	0.023	99.3
3.56-5.03	3.9	0.019	33.6	3433	0.011	0.019	98.7
5.03-56.423	3.7	0.022	25.6	1920	0.013	0.022	98.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 39.25 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	33.03 Å
Translation	2.5 Å	33.03 Å

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Processing

Software

Name	Version	Classification
SCALA	3.3.9	data scaling
PHASER	2.1.4	phasing
PHENIX	dev_1760	refinement
PDB_EXTRACT	3.15	data extraction
Blu-Ice		data collection
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: DsbA wt

Resolution: 1.59→33.032 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.7 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1942	2931	4.97 %	Random selection
R_work	0.158	56028	-	-
obs	0.1598	58959	99.24 %	-

Solvent computation

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

Displacement parameters

B_iso max: 88.98 Å² / B_iso mean: 27.2154 Å² / B_iso min: 10.95 Å²

Refinement step

Cycle: final / Resolution: 1.59→33.032 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2956	0	38	490	3484
B_iso mean	-	-	43.08	38.17	-
Num. residues	-	-	-	-	376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3086
X-RAY DIFFRACTION	f_angle_d	1.247	4180
X-RAY DIFFRACTION	f_chiral_restr	0.056	451
X-RAY DIFFRACTION	f_plane_restr	0.007	547
X-RAY DIFFRACTION	f_dihedral_angle_d	14.507	1134

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 (%)
1.59-1.6161	0.2489	134	0.216	2655	X-RAY DIFFRACTION	99
1.6161-1.6439	0.1961	112	0.1961	2635	X-RAY DIFFRACTION	99
1.6439-1.6738	0.2015	131	0.19	2656	X-RAY DIFFRACTION	99
1.6738-1.706	0.2144	120	0.1861	2688	X-RAY DIFFRACTION	99
1.706-1.7408	0.2342	152	0.1859	2635	X-RAY DIFFRACTION	99
1.7408-1.7787	0.2264	114	0.18	2684	X-RAY DIFFRACTION	100
1.7787-1.8201	0.1804	137	0.1671	2645	X-RAY DIFFRACTION	99
1.8201-1.8656	0.2385	146	0.1746	2638	X-RAY DIFFRACTION	99
1.8656-1.916	0.1979	144	0.1735	2674	X-RAY DIFFRACTION	99
1.916-1.9724	0.1828	160	0.1672	2631	X-RAY DIFFRACTION	99
1.9724-2.036	0.1977	141	0.159	2682	X-RAY DIFFRACTION	99
2.036-2.1088	0.2152	144	0.1574	2671	X-RAY DIFFRACTION	100
2.1088-2.1932	0.1957	148	0.1605	2666	X-RAY DIFFRACTION	100
2.1932-2.293	0.2249	146	0.1575	2676	X-RAY DIFFRACTION	99
2.293-2.4139	0.1878	141	0.155	2660	X-RAY DIFFRACTION	100
2.4139-2.5651	0.1974	131	0.1599	2706	X-RAY DIFFRACTION	100
2.5651-2.763	0.1808	153	0.1518	2668	X-RAY DIFFRACTION	100
2.763-3.0409	0.2053	148	0.1557	2673	X-RAY DIFFRACTION	99
3.0409-3.4805	0.1761	122	0.1471	2709	X-RAY DIFFRACTION	99
3.4805-4.3834	0.1622	161	0.1344	2659	X-RAY DIFFRACTION	99
4.3834-33.032	0.2095	146	0.162	2717	X-RAY DIFFRACTION	98

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	0.7939	0.0825	0.9256	2.8553	1.5977	1.9457	0.1231	0.1994	-0.1696	-0.3362	0.0247	-0.0866	0.0053	0.202	-0.1301	0.207	-0.0225	-0.0156	0.202	-0.0364	0.1684	30.3063	-9.8358	0.5137
2	1.7877	0.5566	0.0378	1.5977	0.0811	2.1305	-0.0454	-0.055	-0.0012	0.0125	0.0061	-0.1295	-0.0348	0.1848	0.0327	0.0994	-0.0339	-0.0218	0.128	0.0004	0.0929	36.451	-1.6075	16.8035
3	1.2052	0.3334	0.2744	3.7441	1.233	2.3273	0.0109	0.2884	-0.0507	-0.4533	0.0607	0.156	-0.1521	0.1463	-0.0725	0.2039	-0.0022	-0.0427	0.2189	-0.0512	0.1682	26.746	-13.349	-4.0361
4	0.8227	0.4447	-0.093	1.7846	1.1833	2.0136	0.0264	0.0725	0.1223	-0.2134	0.0156	0.3037	-0.4433	-0.2704	-0.0354	0.2008	0.024	0.0219	0.1592	0.0232	0.1723	5.7742	0.5765	19.8674
5	7.7891	-3.7312	-1.7201	5.4209	1.4608	4.0056	-0.0307	-0.1276	-0.1866	0.4974	0.0785	0.5947	0.1287	-0.2685	-0.0728	0.2074	-0.009	0.0656	0.1067	0.0088	0.2222	6.0376	-6.074	30.6656
6	2.7266	-1.4286	-1.6877	4.4643	3.0283	6.3216	-0.0138	-0.233	0.181	0.1209	-0.0996	0.5043	-0.1185	-0.483	0.0859	0.1805	-0.0241	-0.0021	0.2971	0.0001	0.2737	0.6705	-6.709	19.0483
7	3.5022	0.3993	-1.5303	2.5587	0.5415	1.3994	-0.0604	0.0352	-0.1695	-0.0368	-0.026	-0.0525	0.0339	0.0085	0.0822	0.1367	-0.0394	-0.0171	0.1561	-0.0021	0.1242	8.0835	-21.0279	14.7467
8	4.4307	-0.1704	2.2974	1.6834	0.3909	4.9082	-0.1093	0.2967	-0.4405	-0.3204	0.1071	0.1063	0.3065	-0.1274	0.0317	0.1457	-0.0914	0.0003	0.245	-0.0059	0.1609	-1.6059	-27.8863	12.1359
9	2.7873	2.405	-0.3644	4.214	0.2351	1.3258	-0.1411	0.199	0.35	-0.7378	0.1624	0.9501	-0.1632	-0.4363	0.0188	0.2391	0.0116	-0.1174	0.2973	0.0709	0.2793	-4.5855	-10.4059	8.4356
10	5.4441	-2.5709	0.4856	5.5543	1.6025	4.9978	0.0735	0.0413	0.6128	-0.5132	0.0862	0.4442	-0.8417	-0.4199	-0.1688	0.2729	0.0311	0.0206	0.1736	0.0451	0.3006	3.2393	2.6431	15.9415
11	4.8674	-0.2645	-0.3386	4.8986	-2.3561	5.8948	-0.1271	-0.1103	0.0561	-0.5222	0.1095	-0.7481	-0.0873	0.8476	-0.0203	0.3256	-0.0554	0.1772	0.2412	-0.09	0.3768	15.2059	5.4136	26.559
12	3.4467	0.8267	1.0871	3.7644	-0.7358	4.6925	0.0757	0.0122	0.3584	0.0966	0.0906	0.3397	-0.2088	-0.3114	-0.1255	0.2743	0.0174	0.1452	0.1189	-0.0108	0.2878	5.4091	3.8092	30.1148

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 65 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 66 through 145 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 146 through 188 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 38 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 39 through 49 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 50 through 65 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 66 through 114 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 115 through 128 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 129 through 144 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 145 through 161 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 162 through 170 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 171 through 188 )	B

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