PDB-7s1c: Crystal structure of E.coli DsbA in complex with compound MIPS-00...

ID or keywords:

Entry

Database: PDB / ID: 7s1c

Title

Crystal structure of E.coli DsbA in complex with compound MIPS-0001897 (compound 1)

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 / Resolution: 1.949 Å

Authors

Heras, B. / Scanlon, M.J. / Martin, J.L. / Sharma, P.

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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7s1c.cif.gz	169.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7s1c_validation.pdf.gz	668 KB	Display	wwPDB validaton report
Full document	7s1c_full_validation.pdf.gz	669.7 KB	Display
Data in XML	7s1c_validation.xml.gz	19 KB	Display
Data in CIF	7s1c_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s1/7s1c ftp://data.pdbj.org/pub/pdb/validation_reports/s1/7s1c	HTTPS FTP

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Related structure data

Related structure data	7s1dC 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

42.6 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)	116.199, 63.701, 74.257
Angle α, β, γ (deg.)	90.000, 126.110, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-408- HOH
2	1	B-457- 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-5VA / ~{N}-methyl-1-(3-thiophen-3-ylphenyl)methanamine Mass: 203.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₃NS / 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.: 313 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.64 Å³/Da / Density % sol: 53.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / 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: 0.95438 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 31, 2009 / Details: mirrors

Radiation

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

Radiation wavelength

Wavelength: 0.95438 Å / Relative weight: 1

Reflection

Resolution: 1.949→50 Å / Num. obs: 32047 / % possible obs: 99.9 % / Redundancy: 3.7 % / B_iso Wilson estimate: 28.73 Å² / R_merge(I) obs: 0.053 / Χ²: 1.058 / Net I/av σ(I): 21.582 / Net I/σ(I): 14.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
1.95-1.98	3.7	0.396	1586	1.095	1	100
1.98-2.02	3.7	0.335	1582	1.086	1	100
2.02-2.06	3.7	0.307	1604	1.096	1	99.9
2.06-2.1	3.7	0.271	1586	1.076	1	100
2.1-2.15	3.7	0.221	1603	1.09	1	99.9
2.15-2.2	3.7	0.175	1603	1.075	1	100
2.2-2.25	3.7	0.162	1573	1.078	1	100
2.25-2.31	3.7	0.15	1608	1.08	1	99.9
2.31-2.38	3.7	0.122	1602	1.073	1	99.9
2.38-2.46	3.7	0.115	1603	1.025	1	99.9
2.46-2.54	3.7	0.099	1599	1.053	1	100
2.54-2.65	3.7	0.083	1604	1.049	1	100
2.65-2.77	3.8	0.067	1601	1.051	1	100
2.77-2.91	3.8	0.06	1584	1.03	1	100
2.91-3.1	3.8	0.049	1594	1.056	1	100
3.1-3.33	3.8	0.041	1607	1.134	1	100
3.33-3.67	3.8	0.033	1632	1.015	1	100
3.67-4.2	3.8	0.03	1596	1.154	1	100
4.2-5.29	3.7	0.031	1635	0.94	1	100
5.29-50	3.6	0.044	1645	0.91	1	98.9

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PDB_EXTRACT	3.15	data extraction
PHENIX	dev_1760	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: DsbA wt

Resolution: 1.949→29.996 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2085	3223	10.06 %
R_work	0.1669	28803	-
obs	0.1711	32026	99.74 %

Solvent computation

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

Displacement parameters

B_iso max: 109.04 Å² / B_iso mean: 37.579 Å² / B_iso min: 15.07 Å²

Refinement step

Cycle: final / Resolution: 1.949→29.996 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2956	0	16	313	3285
B_iso mean	-	-	73.95	44.81	-
Num. residues	-	-	-	-	376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3037
X-RAY DIFFRACTION	f_angle_d	0.959	4103
X-RAY DIFFRACTION	f_chiral_restr	0.037	444
X-RAY DIFFRACTION	f_plane_restr	0.004	534
X-RAY DIFFRACTION	f_dihedral_angle_d	15.42	1109

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 (%)
1.9493-1.9784	0.2503	126	0.2243	1181	X-RAY DIFFRACTION	96
1.9784-2.0093	0.2396	133	0.2025	1285	X-RAY DIFFRACTION	100
2.0093-2.0423	0.2746	140	0.2064	1258	X-RAY DIFFRACTION	100
2.0423-2.0775	0.2524	140	0.1976	1232	X-RAY DIFFRACTION	100
2.0775-2.1153	0.2124	138	0.1924	1243	X-RAY DIFFRACTION	100
2.1153-2.1559	0.2729	138	0.1863	1245	X-RAY DIFFRACTION	100
2.1559-2.1999	0.2229	169	0.1766	1233	X-RAY DIFFRACTION	100
2.1999-2.2477	0.2165	140	0.1751	1234	X-RAY DIFFRACTION	100
2.2477-2.3	0.2499	132	0.1757	1259	X-RAY DIFFRACTION	100
2.3-2.3575	0.2023	144	0.1783	1244	X-RAY DIFFRACTION	100
2.3575-2.4212	0.2336	143	0.182	1243	X-RAY DIFFRACTION	100
2.4212-2.4924	0.2756	139	0.1842	1242	X-RAY DIFFRACTION	100
2.4924-2.5728	0.2557	131	0.1819	1290	X-RAY DIFFRACTION	100
2.5728-2.6647	0.2134	131	0.1809	1249	X-RAY DIFFRACTION	100
2.6647-2.7714	0.2376	152	0.1681	1258	X-RAY DIFFRACTION	100
2.7714-2.8974	0.2387	128	0.1821	1251	X-RAY DIFFRACTION	100
2.8974-3.05	0.2147	143	0.172	1247	X-RAY DIFFRACTION	100
3.05-3.2409	0.2362	143	0.1733	1245	X-RAY DIFFRACTION	100
3.2409-3.4908	0.2067	140	0.1621	1285	X-RAY DIFFRACTION	100
3.4908-3.8414	0.1644	131	0.1381	1248	X-RAY DIFFRACTION	100
3.8414-4.3958	0.171	160	0.1338	1259	X-RAY DIFFRACTION	100
4.3958-5.5326	0.1585	149	0.1445	1265	X-RAY DIFFRACTION	100
5.5326-29.996	0.2105	133	0.1806	1307	X-RAY DIFFRACTION	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	1.14	-0.4309	0.5627	2.9531	1.1459	1.3343	0.0935	0.3024	-0.1503	-0.599	-0.0188	0.2649	-0.0892	0.1556	-0.0579	0.3423	-0.0711	-0.0225	0.3085	-0.0504	0.2388	28.8383	-9.6441	-0.5348
2	1.456	-0.9031	-0.0066	5.8306	2.0088	2.239	0.0234	0.1924	-0.3568	-0.317	0.214	-0.2363	-0.1012	0.321	-0.1185	0.2286	-0.067	0.0122	0.3098	-0.0512	0.2808	35.6971	-6.7672	3.4254
3	2.0333	0.5117	0.5916	1.2262	0.2299	2.0484	-0.0754	-0.0693	-0.0162	-0.0419	0.0782	0.0678	0.0183	-0.0855	-0.0012	0.1784	-0.0512	0.0015	0.1795	-0.0083	0.1475	32.6741	-2.5005	18.8002
4	1.5627	0.3243	-0.7168	1.4471	0.9075	1.4358	-0.1981	0.1092	0.004	-0.2075	0.2354	-0.4253	-0.2327	0.6083	0.0152	0.24	-0.098	0.0355	0.3175	-0.0262	0.2569	42.6073	1.5429	13.3265
5	1.2006	-0.1522	0.31	4.3059	1.1825	2.8412	-0.027	0.2477	-0.0495	-0.6593	-0.0453	0.4799	-0.2388	0.1918	0.0665	0.302	-0.0145	-0.0551	0.3001	-0.0871	0.298	26.8727	-12.13	-4.1949
6	1.1639	0.5956	-0.1983	2.5966	1.0587	1.9014	0.0509	0.0923	0.0972	-0.152	-0.054	0.1021	-0.2029	-0.1722	-0.0171	0.1857	-0.0165	0.0116	0.1915	0.0127	0.2052	6.0995	-9.1449	18.6036
7	1.0633	0.4041	-0.4113	3.0592	1.021	2.2304	0.071	0.125	0.3053	-0.31	0.0065	0.3043	-0.4588	-0.2996	-0.1119	0.2453	0.0393	0.0486	0.2553	0.0483	0.2932	2.8523	-4.2499	18.5895

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 49 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 65 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 114 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 115 through 145 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 146 through 188 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 114 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 115 through 188 )	B

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