PDB-6pd7: Crystal Structure of EcDsbA in a complex with purified morpholine...

ID or keywords:

Entry

Database: PDB / ID: 6pd7

Title

Crystal Structure of EcDsbA in a complex with purified morpholine carboxylic acid 7

Components

Thiol:disulfide interchange protein DsbA

Keywords

OXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA / OXIDOREDUCTASE-INHIBITOR COMPLEX / REFiLX / OXIDOREDUCTASE

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: 1.92 Å

Authors

Ilyichova, O.V. / Bentley, M. / Doak, B. / Scanlon, M.J.

Funding support

Australia, 2items

Citation

Journal: J.Med.Chem. / Year: 2020
Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiL X ).
Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, ...

History

Deposition	Jun 18, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 11, 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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Download

PDBx/mmCIF format	6pd7.cif.gz	202.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6pd7.ent.gz	133.3 KB	Display	PDB format
PDBx/mmJSON format	6pd7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6pd7_validation.pdf.gz	323.5 KB	Display	wwPDB validaton report
Full document	6pd7_full_validation.pdf.gz	323.9 KB	Display
Data in XML	6pd7_validation.xml.gz	1.5 KB	Display
Data in CIF	6pd7_validation.cif.gz	7.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pd/6pd7 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/6pd7	HTTPS FTP

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Related structure data

Related structure data	5qkcC 5qkdC 5qkeC 5qkfC 5qkgC 5qkhC 5qkiC 5qkjC 5qkkC 5qklC 5qkmC 5qknC 5qkoC 5qkpC 5qkqC 5qkrC 5qksC 5qktC 5qkuC 5qkvC 5qkwC 5qkxC 5qkyC 5qkzC 5ql0C 5ql1C 5ql2C 5ql3C 5ql4C 5ql5C 5ql6C 5ql7C 5ql8C 5ql9C 5qlaC 5qlbC 5qlcC 5qldC 5qleC 5qlfC 5qlgC 5qlhC 5qliC 5qljC 5qlkC 5qllC 5qlmC 5qlnC 5qloC 5qlpC 5qlqC 5qlrC 5qlsC 5qltC 5qluC 5qlvC 5qlwC 5qlxC 5qlyC 5qlzC 5qm0C 5qm1C 5qm2C 5qm3C 5qm4C 5qm5C 5qm6C 5qm7C 5qm8C 5qm9C 5qmaC 5qmbC 5qmcC 5qmdC 5qmeC 5qmfC 5qmgC 5qmhC 5qmiC 5qmjC 5qmkC 5qmlC 5qmmC 5qmnC 5qmoC 5qmpC 5qmqC 5qmrC 5qmsC 5qmtC 5qmuC 5qmvC 5qmwC 5qmxC 5qmyC 5qmzC 5qn0C 5qn1C 5qn2C 5qn3C 5qn4C 5qn5C 5qn6C 5qn7C 5qn8C 5qn9C 5qnaC 5qnbC 5qncC 5qndC 5qneC 5qnfC 5qngC 5qnhC 5qniC 5qnjC 5qnkC 5qnlC 5qnmC 5qnnC 5qnoC 5qnpC 5qnqC 5qnrC 5qnsC 5qntC 5qnuC 5qnvC 5qnwC 5qnxC 5qnyC 5qnzC 5qo0C 5qo1C 5qo2C 5qo3C 5qo4C 5qo5C 5qo6C 5qo7C 5qo8C 5qo9C 5qoaC 5qobC 5qocC 5qodC 5qoeC 5qofC 5qogC 6pbiC 6pc9C 6pdhC 6pg1C 6pg2C 6pgjC 6piqC 6pliC 6whdC 1dsbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5qo0-1 5qm6-1 5qmy-1 5qlq-1 5qo0-2 4ocf-2 5qlj-1 5qm2-1 5qo9-2 5qkr-1 5qnx-1 5qmo-1 5qnz-1 5ql8-1 5qmm-1 5qlt-1 5qnv-1 5qls-1 5qne-1 6pg2-1 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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
21.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Thiol:disulfide interchange protein DsbA

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

Unit cell

Length a, b, c (Å)	119.339, 48.822, 91.538
Angle α, β, γ (deg.)	90.000, 117.029, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	B-203- 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 / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical	ChemComp-OAJ / (3R)-4-{[4-(4-cyano-3-methylphenoxy)phenyl]acetyl}morpholine-3-carboxylic acid Mass: 380.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₀N₂O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.81 Å³/Da / Density % sol: 56.22 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 25-35 % PEG MME 2000, 100-300 mM KBr

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2018
Radiation	Monochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95373 Å / Relative weight: 1
Reflection	Resolution: 1.92→43.19 Å / Num. obs: 35961 / % possible obs: 99.6 % / Redundancy: 6.8 % / B_iso Wilson estimate: 28.36 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.076 / R_pim(I) all: 0.048 / R_rim(I) all: 0.09 / Χ²: 1 / Net I/σ(I): 13.1
Reflection shell	Resolution: 1.92→1.97 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.583 / Num. unique obs: 2265 / CC_1/2: 0.888 / R_pim(I) all: 0.373 / R_rim(I) all: 0.695 / Χ²: 0.88 / % possible all: 94.1

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3211	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DSB

1dsb

Resolution: 1.92→43.19 Å / SU ML: 0.2286 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0878

	R_factor	Num. reflection	% reflection
R_free	0.2314	1836	5.11 %
R_work	0.1874	-	-
obs	0.1896	35924	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 42.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→43.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2893	0	28	303	3224

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0097	3054
X-RAY DIFFRACTION	f_angle_d	0.7793	4158
X-RAY DIFFRACTION	f_chiral_restr	0.0446	453
X-RAY DIFFRACTION	f_plane_restr	0.004	548
X-RAY DIFFRACTION	f_dihedral_angle_d	5.4039	2434

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 (%)
1.92-1.97	0.3931	150	0.3175	2455	X-RAY DIFFRACTION	95
1.97-2.03	0.3203	130	0.2658	2640	X-RAY DIFFRACTION	99.89
2.03-2.1	0.3062	130	0.2425	2613	X-RAY DIFFRACTION	99.78
2.1-2.17	0.2793	134	0.22	2611	X-RAY DIFFRACTION	99.82
2.17-2.26	0.2875	130	0.2191	2620	X-RAY DIFFRACTION	99.82
2.26-2.36	0.2602	146	0.2143	2610	X-RAY DIFFRACTION	99.75
2.36-2.49	0.2776	155	0.2059	2633	X-RAY DIFFRACTION	99.89
2.49-2.64	0.2724	137	0.197	2597	X-RAY DIFFRACTION	99.85
2.64-2.85	0.2628	138	0.2086	2644	X-RAY DIFFRACTION	99.89
2.85-3.13	0.2396	147	0.1964	2629	X-RAY DIFFRACTION	99.86
3.13-3.58	0.2248	147	0.1874	2648	X-RAY DIFFRACTION	99.82
3.58-4.52	0.2162	122	0.1524	2680	X-RAY DIFFRACTION	99.86
4.52-43.2	0.1506	170	0.1456	2708	X-RAY DIFFRACTION	99.86

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	5.70852883055	0.859764739994	2.77295821656	6.69487607637	-1.93959167462	2.20054572406	-0.0302028539348	0.667613447741	-0.732327121524	-0.200161788744	0.2053984091	-0.896272816026	1.0318894496	0.37520270219	-0.139433923285	0.610280186728	0.209051609224	-0.0371400328356	0.563909714432	-0.157181898421	0.60064381692	32.5283362564	-10.2064109587	9.71976248383
2	2.62897135311	0.572399674688	0.168091243049	2.74072213193	0.457373878593	2.04860020108	-0.0365352928863	0.0987098705399	-0.264113479875	0.238102246209	0.0585807705515	0.00113580821462	0.236674785453	-0.0989715973774	0.00481083150606	0.334808196991	0.131889634116	0.0197200973379	0.351378251682	0.0154247389346	0.331141686746	27.5359461308	6.60230480727	16.854432771
3	3.20634722004	-0.0865011442353	-0.859260469371	2.50623516134	0.535230711035	3.32035389027	-0.127870314414	0.586666763077	-0.0792757330661	-0.111921311907	0.0354706358984	0.151757382639	0.0356983097416	-0.42769432036	0.0958048533453	0.25344602101	0.100371914226	-0.0128186366565	0.438509099529	0.00954697563407	0.315610358089	26.403790355	8.52924094464	10.8307881995
4	1.74652872725	-0.22505485901	-0.345725807493	1.38891527034	0.373788956999	0.921727475913	0.0105299132432	0.0100773768276	0.162475035724	0.0337426394951	0.00513338938051	-0.0175557832751	-0.133973247812	-0.121978798579	-0.040944598033	0.330285129513	0.160780792908	0.0109601205778	0.300242829687	0.0360222489698	0.307923435046	23.8001185842	23.6143131337	20.7687628414
5	3.71362924701	-3.06396329222	0.471321733364	2.55897600515	-0.66443162508	3.28947740131	0.0535235846281	0.287163299673	-0.276083980604	0.213266818071	-0.260817900565	0.674680294325	0.0592037236096	-0.526594560449	0.189173708879	0.275505825463	0.0120457509898	0.0664269767835	0.289336799341	-0.00752875072267	0.346877396244	14.5492291918	9.07772429154	23.2084785351
6	4.5836395071	1.98932714696	1.70497262795	3.568225608	2.12001949082	3.73363291932	-0.255879000805	-0.071873034609	-0.522929877809	0.329207024272	0.172739104506	-0.0358207826275	0.489286639974	0.0434340535386	0.0726731256324	0.377794635278	0.108138634402	0.0351739606053	0.372294825246	0.0304582599211	0.428490300946	26.0042296055	-1.0229157687	17.7451483365
7	5.25376289471	2.89240654561	-0.570611577849	1.84707081211	-0.72559895872	0.752323621767	-0.193111623976	0.516971986699	-0.810196651478	0.0748855035143	0.334612912392	-0.421880161723	0.231474238629	0.0823492208688	-0.120201190063	0.378795823175	0.13588404971	-0.0306123628494	0.428006670696	-0.139602388022	0.437525228637	34.4641293734	-0.996120244834	7.01081753614
8	6.69873786067	-1.34162717637	-1.57369424708	6.36972271538	-0.85457426355	4.9266502977	0.020994434379	-0.559576516461	0.199807437395	0.701571941583	-0.135077452987	-0.187401918201	-0.206240967792	0.539407976495	0.114337187391	0.372370489892	-0.0156288801597	-0.0212170014	0.435353982389	-0.024486974641	0.229095312666	52.1402622299	18.1406985203	41.4747634068
9	1.3018553079	-0.721033404463	-0.167121446326	3.54094874569	0.524472099009	2.26019861434	0.103898602172	0.0837155257506	0.0872847683025	-0.140077815186	-0.120159142394	0.0238761403651	-0.0534048826453	0.329318296614	0.0209129757122	0.199914648635	0.0526801399439	0.0216743983967	0.383443147707	0.0202842294063	0.238341564106	52.4919534837	20.3732238736	23.8279755948
10	2.64068886613	0.37240011151	-0.0250644565036	1.65126234012	0.353105552078	2.44560151259	-0.0420819066645	0.340592590474	-0.0805291941146	-0.0643540593076	0.0969996108895	-0.0344253506387	-0.034218300245	0.223936854405	-0.0413392898271	0.286204230682	0.0860173510357	-0.00274412723518	0.393566626695	0.00429478653267	0.259423167416	56.3633866508	12.8178528429	9.80698981958
11	2.76279097828	-1.54042004538	-1.93982917507	2.64773703737	1.6279020131	2.58724873702	-0.123822846634	-0.34868702634	-0.324770510038	0.398496527197	0.0460791370378	0.0953856752911	0.304627669052	0.448692058016	0.0944702314245	0.292350157201	0.104356379262	0.000389441128056	0.341609037838	0.0499890810696	0.261737587869	55.3334926912	10.0350098089	29.576643873
12	2.15178290988	2.05923163486	-1.70609188214	2.67705290764	-3.19380601602	4.80390222385	0.0770423849984	0.112999971093	0.94241619939	0.151374603685	0.172980152843	0.572930965568	-0.469624167345	-0.779494849963	-0.160218432698	0.572065948356	0.211947905239	0.0115414122605	0.591351354007	-0.0397709799377	0.535272771933	41.981944248	28.565665397	33.574693364
13	5.8123795166	-0.790699900043	1.05960831433	6.24578793871	-1.33280757146	6.02193307773	-0.0380602976987	-0.505028174968	0.534582839314	0.461642657696	-0.107507223341	-0.270881327714	-1.17337456641	0.305895719861	0.171796629589	0.510366907789	-0.0859643736203	0.0181938326981	0.388040692103	-0.086297411805	0.316960622395	52.5531334505	28.7653641113	35.2383508643

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 128 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 129 through 145 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 146 through 161 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 162 through 188 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 21 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 22 through 65 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 128 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 129 through 161 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 162 through 170 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 171 through 188 )

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