PDB-7s1l: Crystal structure of E.coli DsbA in complex with compound MIPS-00...

ID or keywords:

Entry

Database: PDB / ID: 7s1l

Title

Crystal structure of E.coli DsbA in complex with compound MIPS-0001896 (compound 72)

Components

Thiol:disulfide interchange protein DsbA

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / thioredoxin fold / thiol-disulfide oxidoreductase / inhibitor / DsbA / 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: 1.623 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	Nov 13, 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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PDBx/mmCIF format	7s1l.cif.gz	172.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7s1l.ent.gz	135.9 KB	Display	PDB format
PDBx/mmJSON format	7s1l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7s1l_validation.pdf.gz	749 KB	Display	wwPDB validaton report
Full document	7s1l_full_validation.pdf.gz	754 KB	Display
Data in XML	7s1l_validation.xml.gz	20.7 KB	Display
Data in CIF	7s1l_validation.cif.gz	31.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s1/7s1l ftp://data.pdbj.org/pub/pdb/validation_reports/s1/7s1l	HTTPS FTP

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Related structure data

Related structure data	7s1cC 7s1dC 7s1fC 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

42.8 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
21.5 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)	116.208, 63.944, 74.668
Angle α, β, γ (deg.)	90.000, 126.390, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-481- 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-62J / methyl cis-4-({[3-(thiophen-3-yl)benzyl]amino}methyl)cyclohexanecarboxylate Mass: 343.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₀H₂₅NO₂S / 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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.66 Å³/Da / Density % sol: 53.68 %
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 1, 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: 1.62→37.26 Å / Num. obs: 55151 / % possible obs: 99 % / Redundancy: 3.8 % / R_merge(I) obs: 0.055 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.62→1.67 Å / R_merge(I) obs: 0.584 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4013

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	34.37 Å
Translation	2.5 Å	34.37 Å

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Processing

Software

Name	Version	Classification
PHASER	2.3.0	phasing
PHENIX	dev_1760	refinement
PDB_EXTRACT	3.15	data extraction
xia2		data reduction
xia2		data scaling
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: DsbA wt

Resolution: 1.623→34.368 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.33 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.1899	2800	5.08 %
R_work	0.1609	52350	-
obs	0.1624	55150	98.93 %

Solvent computation

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

Displacement parameters

B_iso max: 87.59 Å² / B_iso mean: 25.5952 Å² / B_iso min: 4.69 Å²

Refinement step

Cycle: final / Resolution: 1.623→34.368 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2956	0	26	427	3409
B_iso mean	-	-	28.12	36.44	-
Num. residues	-	-	-	-	376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	3077
X-RAY DIFFRACTION	f_angle_d	1.534	4161
X-RAY DIFFRACTION	f_chiral_restr	0.081	450
X-RAY DIFFRACTION	f_plane_restr	0.009	542
X-RAY DIFFRACTION	f_dihedral_angle_d	15.024	1124

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 (%)
1.623-1.651	0.2702	146	0.239	2566	X-RAY DIFFRACTION	98
1.651-1.681	0.2622	118	0.228	2587	X-RAY DIFFRACTION	98
1.681-1.7133	0.2494	124	0.2179	2583	X-RAY DIFFRACTION	98
1.7133-1.7483	0.26	154	0.2157	2607	X-RAY DIFFRACTION	99
1.7483-1.7863	0.2274	130	0.2032	2623	X-RAY DIFFRACTION	99
1.7863-1.8278	0.243	128	0.1927	2627	X-RAY DIFFRACTION	99
1.8278-1.8735	0.2381	134	0.1939	2594	X-RAY DIFFRACTION	99
1.8735-1.9242	0.23	137	0.1838	2631	X-RAY DIFFRACTION	99
1.9242-1.9808	0.1973	162	0.1791	2574	X-RAY DIFFRACTION	99
1.9808-2.0447	0.2019	139	0.1541	2629	X-RAY DIFFRACTION	99
2.0447-2.1178	0.1729	147	0.155	2614	X-RAY DIFFRACTION	99
2.1178-2.2026	0.1917	127	0.1487	2648	X-RAY DIFFRACTION	99
2.2026-2.3028	0.1784	148	0.1513	2585	X-RAY DIFFRACTION	99
2.3028-2.4242	0.1737	134	0.1505	2649	X-RAY DIFFRACTION	99
2.4242-2.576	0.1843	150	0.1571	2633	X-RAY DIFFRACTION	99
2.576-2.7748	0.174	145	0.1502	2632	X-RAY DIFFRACTION	99
2.7748-3.0539	0.2141	132	0.1626	2622	X-RAY DIFFRACTION	99
3.0539-3.4955	0.1861	153	0.1463	2634	X-RAY DIFFRACTION	99
3.4955-4.4025	0.1552	140	0.1372	2648	X-RAY DIFFRACTION	99
4.4025-34.368	0.1696	152	0.1571	2664	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	0.4495	0.1291	0.4991	1.2922	0.6208	1.0351	0.0258	0.0937	-0.0415	-0.1828	0.0362	-0.0489	-0.0156	0.1829	-0.0398	0.1659	-0.0137	-0.0085	0.1446	-0.0117	0.1337	30.4774	-9.6114	0.3727
2	0.9729	0.3103	0.0417	0.8416	0.2095	1.2509	-0.0439	-0.0128	0.0173	0.0265	0.0445	-0.0729	-0.0105	0.125	0.0022	0.1211	-0.0269	-0.014	0.1273	0.0071	0.1011	36.3955	-1.6855	16.8953
3	0.8834	-0.0407	0.0955	1.9927	0.4712	1.0502	0.0113	0.2075	-0.0697	-0.259	0.0148	0.1897	-0.0537	0.0729	-0.0262	0.2029	0.0046	-0.0297	0.1683	-0.0347	0.1513	27.0183	-12.9611	-4.6092
4	0.0489	0.0307	-0.1083	0.1359	0.2114	0.9175	0.0951	-0.0117	0.2715	-0.1652	0.006	-0.1287	-0.5217	-0.0203	0.081	0.6077	0.0629	0.2318	0.1136	-0.039	0.5147	6.1515	12.4995	24.9383
5	2.1573	-0.0535	-0.532	1.2551	0.5623	1.3495	0.1358	0.1354	0.1431	0.0561	-0.0431	0.2652	-0.1965	-0.3914	-0.0622	0.1618	0.0115	0.0324	0.2054	0.002	0.2108	5.6328	-4.5684	17.4604
6	0.8231	-0.0442	-0.1571	1.0515	0.6262	2.3423	0.0418	0.0341	0.2549	0.1292	-0.1345	0.328	0.1127	-0.3685	-0.0688	0.1868	-0.0503	0.0714	0.2146	-0.0368	0.2879	2.8615	-6.5566	23.5671
7	4.0564	1.0101	-0.9487	2.0374	-0.1481	0.8261	0.04	0.3581	0.0605	-0.2174	0.0189	0.079	0.0637	-0.0968	0.0166	0.1427	-0.022	-0.0351	0.1811	-0.0048	0.1391	3.0953	-17.4409	10.9607
8	1.3537	0.1944	-0.6794	0.7751	-0.005	0.5778	-0.0223	-0.4094	-0.3731	0.1052	-0.0956	-0.1239	0.0496	0.1432	0.0373	0.1429	-0.0366	0.0062	0.1974	0.0227	0.1926	10.3075	-22.6457	16.7896
9	2.8046	-0.1174	1.5457	1.1417	0.3643	2.5458	-0.1502	0.0316	-0.4627	-0.1255	-0.0203	0.0176	0.1677	-0.0921	-0.0029	0.1467	-0.0617	0.0226	0.2294	0.0399	0.2103	-1.8203	-27.9551	12.4284
10	1.6675	1.7843	-0.196	3.8499	-0.4148	0.7536	-0.0598	0.2113	0.4899	-0.1967	0.0784	0.4393	-0.1099	-0.3372	0.0136	0.1869	0.0272	-0.0643	0.2865	0.0757	0.2732	-4.2198	-9.8508	8.3089
11	2.0927	-1.2024	0.5421	1.8022	0.6379	1.1807	0.2367	0.0209	0.5728	-0.224	0.0257	0.3505	-0.7595	-0.348	-0.0985	0.3137	0.0795	0.0916	0.2312	0.051	0.3832	3.3047	2.5396	15.9188
12	0.2442	0.1115	0.1817	2.5375	-0.7219	0.4032	-0.0395	0.0483	0.0696	-0.0503	-0.0092	-0.2683	-0.1998	0.1621	-0.025	0.4107	-0.1775	0.2821	0.1184	-0.1551	0.5903	14.9696	5.543	26.3254
13	0.8344	0.4976	-0.1385	1.6821	0.6426	2.0734	0.2712	-0.048	0.3512	0.0819	0.1219	0.2411	-0.2883	-0.2712	0.4559	0.3065	0.0206	0.2613	0.0357	-0.2146	0.4626	5.202	3.5983	29.8391

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 11 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 12 through 38 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 39 through 65 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 66 through 82 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 114 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 115 through 128 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 129 through 145 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 146 through 161 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 162 through 170 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 171 through 188 )	B

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