PDB-5ne2: L2 class A serine-beta-lactamase

ID or keywords:

Entry

Database: PDB / ID: 5ne2

Title

L2 class A serine-beta-lactamase

Components

Beta-lactamase

Keywords

HYDROLASE / beta-lactamase / carbapenemase

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: 1.19 Å

Authors

Hinchliffe, P. / Calvopina, K. / Spencer, J.

Citation

Journal: Mol. Microbiol. / Year: 2017
Title: Structural/mechanistic insights into the efficacy of nonclassical beta-lactamase inhibitors against extensively drug resistant Stenotrophomonas maltophilia clinical isolates.
Authors: Calvopina, K. / Hinchliffe, P. / Brem, J. / Heesom, K.J. / Johnson, S. / Cain, R. / Lohans, C.T. / Fishwick, C.W.G. / Schofield, C.J. / Spencer, J. / Avison, M.B.

History

Deposition	Mar 9, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 1, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Jan 17, 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

-
Download

PDBx/mmCIF format	5ne2.cif.gz	314.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ne2.ent.gz	259.3 KB	Display	PDB format
PDBx/mmJSON format	5ne2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ne2_validation.pdf.gz	447.8 KB	Display	wwPDB validaton report
Full document	5ne2_full_validation.pdf.gz	449.7 KB	Display
Data in XML	5ne2_validation.xml.gz	28.1 KB	Display
Data in CIF	5ne2_validation.cif.gz	43.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ne/5ne2 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5ne2	HTTPS FTP

-
Related structure data

Related structure data	5ne1C 5ne3C 1o7eS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ne3-2 1o7e-2 3qji-d 6yrs-1 1iyo-d 6mia-2 2p74-1 4ua6-1 6b1x-2 4f6o-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

-
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

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.678, 84.720, 93.712
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(DE3) (bacteria) / Variant (production host): SoluBL21 / References: UniProt: Q9RBQ1, beta-lactamase
#2: Chemical	ChemComp-DGL / D-GLUTAMIC ACID Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₅H₉NO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49.01 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: Crystal reagent (1.5 uL): 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 ...Details: Crystal reagent (1.5 uL): 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 Protein (1 uL): 42 mg/ml, 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM imidazole, 1 mM TCEP

Crystal

Density Matthews: 2.41 Å³/Da / Density % sol: 49.01 %

Crystal grow

Temperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: Crystal reagent (1.5 uL): 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 ...

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.19→55.92 Å / Num. obs: 176092 / % possible obs: 99.7 % / Redundancy: 8.6 % / CC_1/2: 0.999 / R_pim(I) all: 0.05 / Net I/σ(I): 10.7
Reflection shell	Resolution: 1.19→1.21 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / CC_1/2: 0.625 / R_pim(I) all: 0.778 / % possible all: 98.3

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1O7E

1o7e

Resolution: 1.19→55.916 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.37

	R_factor	Num. reflection	% reflection
R_free	0.164	8701	4.94 %
R_work	0.1522	-	-
obs	0.1528	176092	99.23 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.19→55.916 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4018	0	20	729	4767

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4162
X-RAY DIFFRACTION	f_angle_d	0.963	5666
X-RAY DIFFRACTION	f_dihedral_angle_d	18.883	1535
X-RAY DIFFRACTION	f_chiral_restr	0.076	659
X-RAY DIFFRACTION	f_plane_restr	0.006	758

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 (%)
1.19-1.2035	0.2795	254	0.2798	5472	X-RAY DIFFRACTION	98
1.2035-1.2177	0.2758	255	0.259	5494	X-RAY DIFFRACTION	98
1.2177-1.2325	0.273	269	0.2492	5443	X-RAY DIFFRACTION	98
1.2325-1.2481	0.2596	272	0.2414	5502	X-RAY DIFFRACTION	98
1.2481-1.2646	0.2469	320	0.2365	5448	X-RAY DIFFRACTION	98
1.2646-1.2819	0.2593	269	0.2276	5467	X-RAY DIFFRACTION	99
1.2819-1.3002	0.223	270	0.2147	5560	X-RAY DIFFRACTION	99
1.3002-1.3196	0.215	264	0.2117	5523	X-RAY DIFFRACTION	99
1.3196-1.3402	0.2076	320	0.205	5484	X-RAY DIFFRACTION	99
1.3402-1.3622	0.1997	296	0.1922	5507	X-RAY DIFFRACTION	99
1.3622-1.3857	0.185	304	0.1921	5526	X-RAY DIFFRACTION	99
1.3857-1.4109	0.1981	286	0.1789	5544	X-RAY DIFFRACTION	99
1.4109-1.438	0.1881	276	0.1717	5584	X-RAY DIFFRACTION	99
1.438-1.4674	0.1846	288	0.169	5521	X-RAY DIFFRACTION	99
1.4674-1.4993	0.165	317	0.1553	5567	X-RAY DIFFRACTION	100
1.4993-1.5342	0.175	311	0.152	5556	X-RAY DIFFRACTION	100
1.5342-1.5726	0.1658	305	0.1525	5560	X-RAY DIFFRACTION	100
1.5726-1.6151	0.1541	295	0.1383	5598	X-RAY DIFFRACTION	100
1.6151-1.6626	0.1492	256	0.1416	5655	X-RAY DIFFRACTION	100
1.6626-1.7163	0.1484	297	0.1407	5599	X-RAY DIFFRACTION	100
1.7163-1.7776	0.1504	294	0.1408	5600	X-RAY DIFFRACTION	100
1.7776-1.8488	0.1455	278	0.1376	5626	X-RAY DIFFRACTION	100
1.8488-1.9329	0.1652	265	0.1355	5640	X-RAY DIFFRACTION	100
1.9329-2.0349	0.137	317	0.1375	5661	X-RAY DIFFRACTION	100
2.0349-2.1623	0.1362	283	0.1279	5644	X-RAY DIFFRACTION	100
2.1623-2.3293	0.1365	299	0.1302	5673	X-RAY DIFFRACTION	100
2.3293-2.5637	0.1547	285	0.1268	5667	X-RAY DIFFRACTION	100
2.5637-2.9347	0.1574	304	0.1366	5726	X-RAY DIFFRACTION	100
2.9347-3.6973	0.1488	319	0.1404	5711	X-RAY DIFFRACTION	100
3.6973-55.9775	0.1562	333	0.1476	5833	X-RAY DIFFRACTION	98

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	3.8152	3.0869	2.1875	2.7766	1.7789	6.1171	0.029	0.1871	-0.106	-0.1385	0.0402	0.1609	0.1201	0.0105	-0.0567	0.0874	0.036	-0.0351	0.1535	-0.0023	0.151	66.5215	170.4577	184.558
2	1.0961	0.0298	-0.1449	0.6313	-0.0296	0.2894	0.0372	-0.072	0.0492	0.0689	0.0075	0.0451	-0.0619	-0.0339	-0.033	0.0993	0.0054	0.018	0.0913	-0.01	0.0706	82.5745	176.5914	199.5465
3	2.7174	0.1581	0.235	1.6181	-0.0437	1.0245	-0.0012	-0.0725	-0.0395	0.0529	0.0006	-0.0884	0.0239	0.0832	-0.0071	0.0816	-0.0006	0.0041	0.0995	0.0092	0.0698	103.0321	163.1512	196.7533
4	0.766	-0.5212	-0.101	0.9958	-0.0019	0.3818	-0.0297	-0.1138	-0.0254	0.1484	0.0352	0.0685	-0.0129	-0.0161	-0.004	0.1149	-0.005	0.0134	0.1083	0.0042	0.0851	87.409	169.566	205.1036
5	3.1169	0.1509	0.6571	0.0927	-0.3852	4.6122	0.0439	-0.1174	0.1586	0.0428	0.0364	-0.0873	-0.3023	0.1796	-0.0637	0.1055	-0.0162	0.0133	0.0667	-0.0021	0.0924	97.3504	181.93	196.3923
6	1.4755	0.2875	-0.0644	1.5516	-0.0885	0.6605	0.0334	0.1121	0.019	-0.0715	-0.0213	0.0422	-0.0304	-0.0129	-0.0066	0.083	0.0159	0.0071	0.091	0.0042	0.0769	83.2074	174.4914	188.7778
7	2.5807	1.5245	-0.3479	1.9506	-0.6856	2.5583	0.0675	0.2347	0.0454	-0.1634	-0.0289	0.1656	-0.0238	-0.145	0.0104	0.0795	0.0271	-0.0157	0.1416	-0.0017	0.0939	75.339	173.8246	184.688
8	3.5059	1.352	-0.039	4.485	-0.3756	4.488	-0.0688	0.0702	-0.1285	-0.3718	-0.0701	0.2582	1.2501	-0.2698	0.0393	0.4051	-0.005	0.0234	0.1243	-0.0043	0.1443	109.2517	146.0782	162.3048
9	0.3473	-0.1371	0.178	0.957	0.0854	1.3615	0.0471	0.0145	0.0312	-0.1051	-0.0498	-0.1162	0.0564	0.1487	-0.0252	0.0687	0.0075	0.0112	0.1216	0.0061	0.0986	120.2312	161.6305	174.6443
10	0.828	-0.707	-0.022	2.4073	0.2109	2.4654	0.0085	0.0042	0.0374	0.0061	0.0132	0.0336	-0.1645	0.0678	0.0217	0.0643	-0.0228	0.0141	0.0652	0.0002	0.0786	105.0268	179.1277	182.8984
11	0.5798	-0.307	0.1006	0.6515	0.0854	0.8364	0.0352	0.013	0.043	-0.0287	-0.0558	-0.0783	-0.0436	0.1694	0.0203	0.0854	-0.0142	-0.0042	0.1119	0.0132	0.109	117.9026	175.0413	175.1168
12	1.4308	-0.5456	0.133	2.6966	-1.5609	4.8392	0.0624	0.0991	0.0171	-0.1583	-0.1098	-0.0522	0.0237	0.2524	0.0663	0.0578	-0.0058	0.0068	0.0927	-0.0013	0.0947	120.4927	166.3649	170.3275
13	2.0395	1.3547	-1.1107	3.3208	1.1756	2.6927	0.0064	-0.2544	0.0134	0.1438	-0.0214	-0.1168	-0.009	0.2192	0.0084	0.0724	0.0002	-0.0122	0.1025	0.0119	0.0667	116.884	165.3938	189.9138
14	0.8404	0.052	0.5024	0.9232	-0.265	1.4279	0.037	-0.0338	-0.0462	-0.0329	-0.0399	0.0587	0.1072	-0.0002	-0.0028	0.0891	0.0123	-0.0015	0.0844	-0.0017	0.0884	110.7434	156.2352	176.3808
15	4.2045	-1.4528	3.4783	4.3072	-3.6154	7.5305	-0.0004	-0.0338	-0.0638	-0.2421	-0.0676	-0.0613	0.2412	0.0095	-0.0757	0.0918	0.0053	0.0039	0.0469	-0.0105	0.0603	109.3436	149.6051	170.8216

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 86 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 through 128 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 129 through 194 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 195 through 212 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 213 through 271 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 272 through 291 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 20 through 39 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 86 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 87 through 128 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 129 through 167 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 168 through 194 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 195 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://pdbjlvh1.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