PDB-6qw7: Crystal structure of L2 complexed with relebactam (16 hour soak)

ID or keywords:

Entry

Database: PDB / ID: 6qw7

Title

Crystal structure of L2 complexed with relebactam (16 hour soak)

Components

Beta-lactamase

Keywords

ANTIMICROBIAL PROTEIN / inhibitor / relebactam / diazabicyclooctane / antibiotic resistance.

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Tooke, C.L. / Hinchliffe, P. / Spencer, J.

Funding support

United Kingdom, 1items

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2019
Title: Molecular Basis of Class A beta-Lactamase Inhibition by Relebactam.
Authors: Tooke, C.L. / Hinchliffe, P. / Lang, P.A. / Mulholland, A.J. / Brem, J. / Schofield, C.J. / Spencer, J.

History

Deposition	Mar 5, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 21, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	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
Revision 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6qw7.cif.gz	319.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6qw7.ent.gz	261.8 KB	Display	PDB format
PDBx/mmJSON format	6qw7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6qw7_validation.pdf.gz	753.9 KB	Display	wwPDB validaton report
Full document	6qw7_full_validation.pdf.gz	754.5 KB	Display
Data in XML	6qw7_validation.xml.gz	27.4 KB	Display
Data in CIF	6qw7_validation.cif.gz	42.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qw/6qw7 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/6qw7	HTTPS FTP

-
Related structure data

Related structure data	6qw8C 6qw9C 6qwaC 6qwbC 6qwcC 6qwdC 6qweC 5ne2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6cyn-7 1hzo-2 1g68-d 4hbt-d 4yfm-2 6v6g-d 6cyn-2 7d5j-1 5ne3-2 3bfd-4 3bfd-3 3bff-3 3bfg-3 4pm7-d 6d7i-d 4zbe-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#164 - Aug 2013 Serotonin Receptor similarity (5) #220 - Apr 2018 Dehalogenases similarity (2) #29 - May 2002 Penicillin-binding Proteins similarity (3) #111 - Mar 2009 Hydrogenase similarity (2) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

defined by author
Evidence: gel filtration
29.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.958, 84.340, 94.136
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-lactamase Mass: 29318.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: blaL2, L2 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Solu / References: UniProt: Q9RBQ1, beta-lactamase
#2: Chemical	ChemComp-DSN / D-SERINE Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#3: Chemical	ChemComp-MK7 / (2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide / MK-7655, bound form Mass: 350.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₂N₄O₆S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.06 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M DL-Glutamic acid; 0.02 M DL-Alanine; 0.02 M Glycine; 0.02 M DL-Lysine; 0.02 M DL-Serine, 0.1 M bicine/Trizma base pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.78→62.82 Å / Num. obs: 54128 / % possible obs: 100 % / Redundancy: 12.7 % / R_pim(I) all: 0.104 / Net I/σ(I): 7.8
Reflection shell	Resolution: 1.78→1.82 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2723 / R_pim(I) all: 0.482

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NE2

5ne2

Resolution: 1.78→62.816 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.48

	R_factor	Num. reflection	% reflection
R_free	0.205	2725	5.04 %
R_work	0.1593	-	-
obs	0.1616	54050	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.78→62.816 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4018	0	30	619	4667

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4205
X-RAY DIFFRACTION	f_angle_d	1.07	5727
X-RAY DIFFRACTION	f_dihedral_angle_d	13.55	2566
X-RAY DIFFRACTION	f_chiral_restr	0.058	668
X-RAY DIFFRACTION	f_plane_restr	0.008	761

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 (%)
1.78-1.8124	0.2928	148	0.2641	2648	X-RAY DIFFRACTION	100
1.8124-1.8472	0.313	152	0.2567	2659	X-RAY DIFFRACTION	100
1.8472-1.885	0.2971	150	0.2469	2663	X-RAY DIFFRACTION	100
1.885-1.9259	0.3004	123	0.22	2685	X-RAY DIFFRACTION	100
1.9259-1.9707	0.2534	146	0.2032	2653	X-RAY DIFFRACTION	100
1.9707-2.02	0.225	139	0.1919	2678	X-RAY DIFFRACTION	100
2.02-2.0747	0.2073	135	0.1741	2686	X-RAY DIFFRACTION	100
2.0747-2.1357	0.1982	148	0.1599	2661	X-RAY DIFFRACTION	100
2.1357-2.2046	0.2241	134	0.1471	2687	X-RAY DIFFRACTION	100
2.2046-2.2834	0.1811	118	0.1443	2705	X-RAY DIFFRACTION	100
2.2834-2.3749	0.1661	132	0.1367	2692	X-RAY DIFFRACTION	100
2.3749-2.483	0.1998	151	0.1388	2706	X-RAY DIFFRACTION	100
2.483-2.6139	0.2109	153	0.1415	2677	X-RAY DIFFRACTION	100
2.6139-2.7776	0.197	162	0.1418	2672	X-RAY DIFFRACTION	100
2.7776-2.9921	0.1832	130	0.1519	2723	X-RAY DIFFRACTION	100
2.9921-3.2932	0.1871	155	0.1497	2713	X-RAY DIFFRACTION	100
3.2932-3.7697	0.2022	128	0.1279	2758	X-RAY DIFFRACTION	100
3.7697-4.7491	0.1532	166	0.1184	2755	X-RAY DIFFRACTION	100
4.7491-62.8553	0.19	155	0.1687	2904	X-RAY DIFFRACTION	100

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	3.1438	1.0335	1.0395	1.2536	0.4374	1.6764	0.0881	0.0783	0.0202	-0.0479	-0.0165	0.3807	0.07	-0.0974	-0.0376	0.0717	0.0521	0.0163	0.1032	0.0069	0.1579	0.6241	5.5829	1.8241
2	2.6066	0.2176	-0.4778	1.4566	0.0412	0.2078	0.0875	-0.2784	0.0733	0.155	-0.0065	0.0173	-0.0079	-0.0559	-0.0502	0.1117	0.0027	0.019	0.1047	-0.0143	0.0546	15.907	5.2265	14.1192
3	6.8911	0.7464	-0.4499	6.1987	-2.0328	4.6473	0.0588	-0.3326	-0.0867	0.4822	-0.0291	-0.3509	-0.0103	0.3181	-0.0769	0.0858	0.0273	-0.0433	0.1662	0.0054	0.0683	37.135	-4.7818	14.5583
4	8.5226	0.1369	-1.7198	1.6174	-0.5973	1.3421	-0.1451	0.2202	-0.3072	-0.0039	0.1191	-0.0078	0.1606	0.0355	0.1055	0.1356	-0.017	-0.0064	0.066	0.0047	0.1281	30.6714	-12.929	5.5538
5	1.7847	-0.6641	-0.4927	1.4605	0.3853	0.5488	-0.0273	-0.2241	-0.0651	0.2435	0.0245	-0.0181	0.0317	0.0892	0.0142	0.1203	-0.0053	-0.0041	0.1062	0.019	0.0734	24.6006	-1.3369	15.4683
6	2.0334	-0.0741	-0.8125	2.0171	-0.1434	1.5765	0.0005	-0.2184	0.0902	0.1923	0.0126	0.03	-0.0133	0.0708	-0.0166	0.0895	0.01	-0.0078	0.078	-0.0163	0.0524	18.6467	6.1428	13.23
7	3.7886	-0.5022	0.7097	3.4612	0.9135	0.6523	0.1402	0.3307	-0.1545	-0.1476	-0.1018	0.0128	-0.1484	0.2254	-0.0266	0.0872	-0.004	0.0191	0.13	0.0027	0.0574	16.198	4.9321	-4.081
8	2.2564	0.5871	0.1696	2.1378	0.1647	1.1404	0.0538	0.0382	0.0024	-0.0306	0.016	0.085	-0.0266	-0.0555	-0.0517	0.0501	0.0208	0.0195	0.0762	0.0049	0.083	12.2939	4.9338	3.4083
9	4.7844	2.2848	-0.2504	2.1645	-0.8822	4.4302	0.1269	0.3375	-0.1075	-0.5024	0.0047	0.0661	0.0623	-0.1842	-0.0052	0.0307	0.0422	-0.0248	0.1364	-0.0196	0.1191	5.456	4.168	-2.6923
10	0.5664	0.4803	0.0387	2.4705	0.0191	2.4873	0.0351	0.1764	0.084	-0.4153	-0.1587	-0.0159	0.7305	0.249	-0.0151	0.2158	0.0374	0.0193	0.0989	-0.0245	0.1165	47.6129	-18.1155	-20.2005
11	1.492	-0.1772	0.761	5.0102	3.8568	3.9015	-0.0055	-0.0188	0.083	0.0292	0.1992	-0.2652	-0.1661	0.2727	-0.1717	0.0686	-0.0307	-0.0034	0.1117	-0.0025	0.131	47.8071	3.316	-5.2898
12	2.7515	-2.4659	1.2147	5.2696	-1.9884	2.7175	-0.1264	0.0286	0.3421	0.1802	0.0768	-0.0876	-0.3237	0.4342	0.117	0.1002	-0.0501	0.0362	0.1327	-0.0319	0.1206	38.9285	13.955	-1.6617
13	0.5068	-0.3727	-0.3648	1.1084	0.1127	1.2176	0.0224	0.0112	0.038	-0.0175	-0.0208	-0.0445	-0.0198	0.1056	0.0152	0.0532	-0.0153	-0.0149	0.0886	-0.0088	0.1163	44.616	2.1512	-9.205
14	1.8836	-0.0883	1.1507	1.23	-0.3594	3.5449	0.0173	-0.0962	-0.0628	0.0415	0.0044	0.0992	0.0911	-0.0595	-0.0391	0.0726	0.0148	-0.0034	0.0509	-0.0076	0.0929	41.0633	-13.2134	-11.1064
15	3.9705	-2.7793	3.1233	2.1991	-2.5477	2.9339	-0.1213	-0.1852	-0.1994	-0.1307	0.0773	0.0098	0.1309	-0.2003	-0.339	0.1834	0.0053	-0.0137	0.0925	-0.0099	0.109	39.553	-19.8589	-16.659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 55 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 56 through 86 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 through 101 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 102 through 115 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 116 through 167 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 168 through 212 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 213 through 228 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 229 through 271 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 272 through 291 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 20 through 68 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 69 through 86 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 87 through 101 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 102 through 212 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 213 through 271 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 272 through 291 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi