PDB-6skr: OXA-10_ETP. Structural insight to the enhanced carbapenem efficie...

ID or keywords:

Entry

Database: PDB / ID: 6skr

Title

OXA-10_ETP. Structural insight to the enhanced carbapenem efficiency of OXA-655 compared to OXA-10.

Components

Beta-lactamase

Keywords

ANTIBIOTIC / Class D beta-lactamase / crystal structures / Carbapenemases / Antibiotic resistance.

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Leiros, H.-K.S.

Citation

Journal: Febs Open Bio / Year: 2020
Title: Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10.
Authors: Leiros, H.S. / Thomassen, A.M. / Samuelsen, O. / Flach, C.F. / Kotsakis, S.D. / Larsson, D.G.J.

History

Deposition	Aug 16, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2	Sep 9, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6skr_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
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Data in CIF	6skr_validation.cif.gz	39.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sk/6skr ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6skr	HTTPS FTP

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Related structure data

Related structure data	6skpC 6skqC 4s2oS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1e4d-1 1k57-2 1k55-2 4wz5-1 1k56-2 1k54-2 5moz-d 2hpb-d 5fq9-d 3nav-d 1e3u-1 1k4e-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: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	48.388, 94.776, 125.588
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Beta-lactamase Mass: 29581.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: blaoxa-10, blaOXA-10, oxa-10, BK373_28375, CQP61_30695, E4Z89_25540, FORC82_p097 Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: Q7BNC2, beta-lactamase
#2: Chemical	ChemComp-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED Mass: 477.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₂H₂₇N₃O₇S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.62 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 11.8 mg/ml 20-23% PEG 3350 0.2 M magnesium formate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.85→25 Å / Num. obs: 50164 / % possible obs: 99.9 % / Redundancy: 7.4 % / B_iso Wilson estimate: 23.02 Å² / CC_1/2: 0.996 / R_rim(I) all: 0.168 / Net I/σ(I): 8.5
Reflection shell	Resolution: 1.85→1.89 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3035 / CC_1/2: 0.42 / R_rim(I) all: 1.705 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
PHENIX	1.14_3260	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4s2o

4s2o

Resolution: 1.85→24.28 Å / SU ML: 0.2206 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.6186

	R_factor	Num. reflection	% reflection
R_free	0.2267	2482	4.96 %
R_work	0.1786	-	-
obs	0.181	50074	99.87 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.62 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→24.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3876	0	74	444	4394

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0115	4120
X-RAY DIFFRACTION	f_angle_d	1.3396	5578
X-RAY DIFFRACTION	f_chiral_restr	0.0612	609
X-RAY DIFFRACTION	f_plane_restr	0.0083	712
X-RAY DIFFRACTION	f_dihedral_angle_d	4.9128	3348

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 (%)
1.85-1.89	0.3529	145	0.3122	2556	X-RAY DIFFRACTION	99.56
1.89-1.92	0.3086	143	0.2919	2619	X-RAY DIFFRACTION	99.93
1.92-1.97	0.2763	146	0.2639	2592	X-RAY DIFFRACTION	99.93
1.97-2.01	0.2897	118	0.2341	2643	X-RAY DIFFRACTION	99.93
2.01-2.06	0.2518	127	0.2178	2602	X-RAY DIFFRACTION	99.96
2.06-2.12	0.2141	153	0.2089	2609	X-RAY DIFFRACTION	99.96
2.12-2.18	0.2421	132	0.1994	2613	X-RAY DIFFRACTION	100
2.18-2.25	0.2538	134	0.1865	2627	X-RAY DIFFRACTION	99.89
2.25-2.33	0.2418	135	0.1904	2621	X-RAY DIFFRACTION	99.96
2.33-2.42	0.2527	142	0.1814	2652	X-RAY DIFFRACTION	99.96
2.42-2.53	0.2415	121	0.1806	2631	X-RAY DIFFRACTION	99.82
2.53-2.67	0.2034	139	0.1726	2627	X-RAY DIFFRACTION	99.78
2.67-2.83	0.2663	134	0.1731	2661	X-RAY DIFFRACTION	100
2.83-3.05	0.2134	128	0.1691	2663	X-RAY DIFFRACTION	100
3.05-3.36	0.2272	125	0.1678	2674	X-RAY DIFFRACTION	99.96
3.36-3.84	0.1973	142	0.1517	2689	X-RAY DIFFRACTION	99.89
3.84-4.84	0.1789	140	0.1336	2727	X-RAY DIFFRACTION	99.86
4.84-24.28	0.2191	178	0.1766	2786	X-RAY DIFFRACTION	99.3

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	8.3344378076	-3.41844505436	1.22881942065	2.7344412217	-0.855298768021	3.41856076571	-0.0347056523443	0.469446463072	0.811190365215	0.0163780559788	-0.22530601565	-0.539659334618	-0.487475065097	0.537025374252	0.237296049747	0.351399231235	-0.119234742121	0.0195656551022	0.322662131649	0.095310783338	0.273291470995	23.4004216557	3.42509236057	-17.600250626
2	1.3787987115	1.21831176689	-1.90424186038	2.52362970301	-1.64702486422	5.0026495359	-0.0414307193085	0.0915380594715	0.0587924871324	-0.133004471979	0.0737506200642	0.0648060717531	-0.2837118797	-0.23605286254	0.000955076618884	0.0929671933917	0.00128417511708	-0.0341113983617	0.129225237734	-0.000183768992091	0.129625351625	14.3168756136	-5.55311265825	-8.86406941175
3	7.52003205819	-3.38481331117	0.5802157925	1.71015526709	0.5031680937	3.07713277484	-0.447739133787	-0.823834256136	0.0163925757904	0.252701687735	0.342307247164	0.0206637500267	0.18712242915	-0.140119120558	0.111302454833	0.167932916601	0.025635740111	0.0603274303872	0.192813776531	0.00125922680014	0.20391287494	14.3064778617	-18.3644576533	14.2967153892
4	1.40475453633	-2.528068373	-0.957774357888	6.07140426579	-0.424375657121	3.91872220718	-0.0937048685126	-0.128655534543	0.179350146563	0.203371912694	0.217879362241	-0.522216748388	-0.160564353592	0.544033496975	-0.0929841044907	0.0914016193002	-0.0122292808453	-0.00660852047281	0.222323555451	-0.0482173045343	0.164899989017	21.3805603439	-13.5429447104	11.4430721825
5	0.474872317806	0.183203858822	-0.22442488047	1.94816449022	-0.167831907647	2.28277716263	-0.0395845630164	-0.0120161282971	0.032881541006	-0.0126076197768	0.0767261189184	0.169029416371	-0.11841685552	-0.216588216652	-0.0233230672769	0.051286145021	0.013322629265	-0.00752169756464	0.160662384157	-0.0037054291037	0.135685092729	8.44578056243	-12.3021515821	-0.79831457999
6	3.84922416907	-0.314431855219	-0.585584720941	1.27985636166	1.31293104695	4.21333791186	0.181959939902	-0.167670746456	0.318160249317	-0.197666678831	-0.190648089714	-0.0909555084201	-0.77870954537	-0.0143921864309	0.0170015701748	0.233887337441	-0.0561048256039	0.00252993964124	0.17691669912	-0.00678537845996	0.183060786268	18.8186108154	1.26220798815	2.57065004846
7	4.05939754636	-2.58214038539	-0.775328637498	5.72334262764	1.19831356932	4.55161918848	0.148229020901	0.218936263761	-0.0908576949061	-0.164363154869	-0.0638438217573	-0.168816977822	-0.0108313453414	0.370327034019	-0.089297437752	0.108823435776	-0.0300754848121	-0.0263330692825	0.178503501426	0.00937970291861	0.115036650532	23.2912383844	-10.0751997345	-8.69415808269
8	4.06240235997	-2.26867933187	-1.58225327212	3.65661277052	1.94509163609	4.39368684394	0.240284652156	-0.0958668724646	0.402753208492	-0.282707640336	0.00482357127466	-0.31288376854	-0.712201797543	0.00775812969728	-0.244288039566	0.190968260444	-0.0355911420221	0.0225916049495	0.149340161569	0.0439990534832	0.170374691741	19.7416247088	-0.152632350446	-6.98453834444
9	7.07867343566	-6.48264968499	1.42799955277	2.05538195425	-3.31972255378	4.00310866713	-0.106609497466	-0.214419412346	0.505930766223	0.331522580729	0.136376633322	-0.727264858075	-0.551399958007	0.237714866602	-0.0535083022633	0.238158889696	-0.103923630835	-0.0267276871491	0.20069332215	-0.00754311409867	0.274495947096	27.2759047868	1.47288091797	-6.33839717738
10	6.41533980947	4.08058364639	-1.17274476904	8.37925474447	-1.98225564654	4.04492083847	-0.258767025132	-0.303165333846	0.349475194529	-0.0529552136188	0.0467644124331	-1.329740809	-0.539400529063	0.992369975039	0.280320706728	0.398982364459	-0.114364212824	-0.0091112327677	0.576554039259	-0.167638516223	0.60869492098	25.1821851778	6.11335979961	38.0514053873
11	2.05555872914	-1.2096973383	0.642540924875	1.99855307847	-0.267120558762	4.38292283064	0.211604748503	-0.0810417873145	0.287666623524	-0.235644114268	-0.0976901289722	-0.0195340911347	-0.612886453328	0.217200575856	-0.087215904319	0.336670640051	-0.0279805183393	0.0892138291688	0.212425818371	-0.0468524084409	0.206337162719	11.8705621604	8.75133218437	30.7676959171
12	0.588818342215	-0.694058905501	-0.0670792810121	1.27076928924	-0.51992446337	0.80192653253	-0.143072853451	0.0759531754909	0.37298446657	-0.966570208321	0.103176884436	0.124255721089	-1.1024923699	-0.026372299323	0.0737474688601	1.33005697967	0.191716577634	0.0308774562313	0.442118451519	-0.0302422830926	0.438279975083	3.08184048671	18.4679200076	8.03291411471
13	0.492639745305	0.221707809015	0.790681300362	3.38916395036	0.821827378482	1.40683779509	-0.244649663099	0.0436097224872	0.177660933659	-0.690504445591	0.195388955067	-0.11173413194	-1.35010020606	0.0861497461516	0.00106318673468	1.2836694746	0.276481141677	0.113057932188	-0.121040751491	-0.0498516437909	0.396044301646	7.36389756016	19.254689265	12.3727496001
14	2.22328218016	0.0129818884494	0.186025914604	2.07581984841	0.509523640077	3.12086459602	0.251837115116	-0.0191308142822	0.304705863788	-0.214866165584	-0.0989093796778	0.190984424438	-0.760310675684	-0.321666240117	-0.11795076257	0.405264645697	0.0714700693692	0.0490073746547	0.18078824673	-0.0276078287972	0.217486441611	5.03763901514	8.9493086648	23.8534630023
15	3.35324544794	-0.544958247727	-0.0969571295922	9.80474987765	2.70286047629	2.9703803108	0.141797688393	-0.452296348568	0.634295284623	-0.00466925087047	0.116044371062	-0.350981951225	-1.07002322212	0.413415891258	-0.285439988008	0.625521244096	-0.124238033385	0.1495441069	0.285830923271	-0.0812424089046	0.289482457471	16.5705046888	15.1946325049	28.6056319334
16	1.39906834467	1.48489314988	1.4138889531	7.96934200469	1.67103125652	1.84980155873	0.330422336943	-0.113203167889	0.290555838792	-0.152272533757	0.0157419844588	-0.613725503035	-0.558839346125	0.740697998715	-0.307752101661	0.420482831622	-0.154936836154	0.209627279522	0.337190569398	-0.121472971389	0.356779961213	19.0275410335	7.37736740345	28.2122647557
17	3.13430965895	-0.0609227292767	0.385608541524	2.00602131693	-1.69645511504	2.95334871816	0.457339891517	0.0625277604911	0.169765716711	-0.369018319591	-0.182421607626	-1.19050800004	-0.692369168964	0.766022016537	-0.140682424294	0.457900346165	-0.237470394251	0.231400386017	0.603424318541	-0.170644503059	0.536313583372	26.1310281847	10.1249045905	26.7683981883

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 79 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 116 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 117 through 197 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 198 through 208 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 209 through 228 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 229 through 243 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 244 through 265 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 20 through 35 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 36 through 79 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 80 through 99 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 100 through 127 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 128 through 208 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 209 through 228 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 229 through 243 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 244 through 265 )

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