PDB-6twj: Apo structure of the Ectoine utilization protein EutD (DoeA) from...

ID or keywords:

Entry

Database: PDB / ID: 6twj

Title

Apo structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongata

Components

Ectoine hydrolase DoeA

Keywords

HYDROLASE / Pita bread / ectoine degradation

Function / homology

Function and homology information

ectoine hydrolase / ectoine catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / Hydrolases; Acting on peptide bonds (peptidases) / hydrolase activity / cytoplasm
Similarity search - Function

Biological species

Halomonas elongata (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Mais, C.-N. / Altegoer, F. / Bange, G.

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex.
Authors: Mais, C.N. / Hermann, L. / Altegoer, F. / Seubert, A. / Richter, A.A. / Wernersbach, I. / Czech, L. / Bremer, E. / Bange, G.

History

Deposition	Jan 13, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 20, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 27, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jul 15, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Jan 24, 2024	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	6twj.cif.gz	383.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6twj_validation.pdf.gz	440.7 KB	Display	wwPDB validaton report
Full document	6twj_full_validation.pdf.gz	454.8 KB	Display
Data in XML	6twj_validation.xml.gz	31.6 KB	Display
Data in CIF	6twj_validation.cif.gz	44.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/6twj ftp://data.pdbj.org/pub/pdb/validation_reports/tw/6twj	HTTPS FTP

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Related structure data

Related structure data	6twkC 6twlC 6twmC 6yo9C 2bwsS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6twk-d 6tsc-1 4s00-2 4s01-1 6yo9-d 4s01-2 6rka-2 6gew-1 4rzy-1 6fbp-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Ectoine hydrolase DoeA

B: Ectoine hydrolase DoeA

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	120.370, 123.140, 61.490
Angle α, β, γ (deg.)	90.000, 97.184, 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

#1: Protein	Ectoine hydrolase DoeA / Putative peptidase Mass: 45881.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halomonas elongata (bacteria) / Gene: doeA, A8U91_03446, DKQ62_09665 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1B8NWR1, UniProt: E1V7W1*PLUS, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Ectoine hydrolase DoeA / Putative peptidase

Mass: 45881.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Halomonas elongata (bacteria) / Gene: doeA, A8U91_03446, DKQ62_09665 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1B8NWR1, UniProt: E1V7W1*PLUS, Hydrolases; Acting on peptide bonds (peptidases)

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.51 Å³/Da / Density % sol: 51.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate, 20% (wt/vol) PEG 3350 / PH range: 6.5-7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 6, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 2.15→47.72 Å / Num. obs: 47539 / % possible obs: 98.26 % / Redundancy: 3 % / B_iso Wilson estimate: 36.59 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.087 / Net I/σ(I): 8.96
Reflection shell	Resolution: 2.15→2.227 Å / R_merge(I) obs: 0.6207 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 4593 / CC_1/2: 0.659

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Processing

Software

Name	Version	Classification
Coot	1.17.1_3660	model building
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2BWS

2bws

Resolution: 2.15→43.34 Å / SU ML: 0.3111 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4782

	R_factor	Num. reflection	% reflection
R_free	0.2624	2371	5 %
R_work	0.2277	-	-
obs	0.2294	47400	98.27 %

Solvent computation

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

Displacement parameters

B_iso mean: 41.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→43.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6158	0	0	274	6432

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0048	6344
X-RAY DIFFRACTION	f_angle_d	0.7607	8633
X-RAY DIFFRACTION	f_chiral_restr	0.0483	894
X-RAY DIFFRACTION	f_plane_restr	0.0063	1121
X-RAY DIFFRACTION	f_dihedral_angle_d	5.9234	858

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 (%)
2.15-2.19	0.3616	136	0.3288	2579	X-RAY DIFFRACTION	96.83
2.19-2.24	0.3421	136	0.3123	2588	X-RAY DIFFRACTION	97.32
2.24-2.29	0.3383	141	0.2999	2685	X-RAY DIFFRACTION	99.12
2.29-2.35	0.3466	141	0.2606	2668	X-RAY DIFFRACTION	99.72
2.35-2.41	0.2771	142	0.265	2691	X-RAY DIFFRACTION	99.47
2.41-2.49	0.2811	139	0.2522	2648	X-RAY DIFFRACTION	99.5
2.49-2.57	0.2881	142	0.2553	2688	X-RAY DIFFRACTION	99.51
2.57-2.66	0.273	141	0.2573	2682	X-RAY DIFFRACTION	99.72
2.66-2.76	0.3013	141	0.2466	2681	X-RAY DIFFRACTION	99.54
2.76-2.89	0.2975	141	0.2319	2674	X-RAY DIFFRACTION	99.08
2.89-3.04	0.277	139	0.2269	2648	X-RAY DIFFRACTION	98.48
3.04-3.23	0.2723	138	0.2317	2627	X-RAY DIFFRACTION	97.19
3.23-3.48	0.2575	137	0.2116	2605	X-RAY DIFFRACTION	97.2
3.48-3.83	0.2239	140	0.1966	2651	X-RAY DIFFRACTION	97.83
3.83-4.39	0.2214	138	0.1967	2624	X-RAY DIFFRACTION	96.4
4.39-5.53	0.2504	138	0.2099	2614	X-RAY DIFFRACTION	96.43
5.53-47.72	0.241	141	0.2268	2676	X-RAY DIFFRACTION	97.27

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	4.06316879559	-0.0192737985481	0.117211925036	0.606135058849	0.619686340235	3.37162441733	-0.0819192982985	-0.182032496537	0.0418076103604	0.0182079031188	-0.152168139671	-0.149655232792	-0.231103121172	-0.17342456157	0.235143741505	0.336490563548	-0.0324329886072	-0.00147717900123	0.232330337847	-0.0387740159567	0.266744588454	5.75974773776	89.8460608723	32.8404738504
2	2.61356453924	-1.08674574884	-0.230411270268	2.08110142764	0.377712657018	2.31355128824	0.0896591315851	-0.245008303021	0.465120182542	-0.247392247948	-0.0130327457804	-0.22786185495	-0.500303441396	0.20446409564	-0.0363173051172	0.434018342127	-0.103391663923	0.0318958661332	0.298718860982	-0.0491149351417	0.27855570814	18.0204021104	99.4963786785	33.3992757776
3	1.5941953534	0.29915268176	0.960105007228	0.91242753794	0.276257013177	1.82179300581	0.0227792817586	-0.495262499893	0.111172893082	0.10490839223	-0.055458768446	-0.0444120474363	-0.223565517443	0.00444048275707	0.0052607599582	0.341445962968	-0.0584985326321	-0.0015787559188	0.449299253217	-0.0193572599867	0.293075153642	16.4972211135	90.2705285889	43.1650844561
4	3.91066080515	-0.796791031185	-1.16162246069	1.12968045382	0.222454218482	1.1272513091	-0.0167370644841	0.545995247042	-0.150832725097	-0.316140899519	0.000154041762455	0.112809820042	0.0659192053356	-0.0729742736379	0.0387486070008	0.311604383513	-0.0413723427331	-0.0417265013398	0.314644249493	-0.0296970114848	0.249136015251	19.6145434958	78.4541382217	7.76816333354
5	3.04871320407	0.25058896899	-1.00773544387	3.17948413796	1.06739483165	1.71359276897	0.0496735376077	0.371964367036	-0.192098553025	-0.129209262278	-0.136120900001	-0.0517978475625	0.323608674755	-0.0484537085333	0.0311031987419	0.312032207534	-0.0226413789719	0.0182949113129	0.311825787524	-0.0417699689402	0.220885175616	24.6057603331	75.7141690025	11.796889385
6	2.57743545555	1.01003143846	-1.46509468759	0.514149168132	-0.276385018638	2.33016954392	-0.279366752979	-0.0146416832002	-0.892524486121	-0.18150577018	-0.216837587948	-0.262364460428	0.688387225923	0.32944346428	0.449215243844	0.513393239855	0.0724308564685	0.0288333030368	0.339825152505	0.0596353563177	0.505597067347	17.890627519	62.7229930076	13.1579299807
7	3.76983369939	-0.399264072466	-0.35676430895	4.35160344321	1.4509065602	5.50070993228	0.00886199801224	-0.122612340042	0.0935664840062	0.288967028939	-0.00438734658229	0.426006636183	0.694470224754	-0.0525505991341	-0.0376012886403	0.359776356948	-0.0359835279715	0.0676274220102	0.203138408077	0.023185401786	0.450034494967	8.0129580969	58.4601584704	25.7444428748
8	2.73756592254	0.311192282596	0.479651218834	1.40882973363	-1.28455173153	1.89564717279	-0.0593441970033	-0.0820086618614	-0.235080308284	0.188435554802	-0.0725852359824	0.185366324274	0.0251879092045	0.104857623574	0.115497368834	0.240431903345	-0.00831444171675	0.0285768516033	0.202048138912	0.0189085779453	0.308509486507	11.8797890366	71.7460645119	27.0032751116
9	1.96686889206	0.336800161794	-1.95882845166	3.27982235574	0.66507438201	3.67092290079	-0.134766743726	-0.223837686015	-0.376485483399	-0.0592407410664	0.209924500892	-0.209153360431	0.404278257327	0.543931729474	-0.0452889841339	0.382179421268	0.0225129961516	-0.00215080455841	0.326620021126	-0.0377413423986	0.37104744819	15.5958064524	65.3400153208	14.5604867096
10	1.63208047146	-0.430253080725	0.746820580607	0.736962855999	-0.36518858459	2.22367853496	0.04269942943	-0.123589421115	-0.108616391339	-0.0237425559541	0.0199598627385	-0.0342589521223	0.178779280092	-0.156038201865	-0.0429326897238	0.205141226362	-0.0639805139078	0.0152319108925	0.194693693314	-0.0435332942222	0.220844020184	35.2067353039	86.0447850265	25.5498801008
11	0.785327260629	1.10249240174	0.484020692481	2.35515984697	0.628214818146	3.42191608812	0.0650255703824	-0.108866409607	0.284020453809	0.156960591419	-0.0824403904583	0.0190512998294	-0.423174246713	-0.254037888035	0.0748756350936	0.266319692179	0.0281860240485	0.0234924810658	0.244673776581	-0.0498272965668	0.370205437248	40.0234030099	103.941155319	22.3480297677

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 44 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 163 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 164 through 207 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 208 through 260 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 261 through 297 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 298 through 317 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 318 through 362 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 363 through 399 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 4 through 297 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 298 through 398 )

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