PDB-6b2n: Crystal structure of TEM-1 beta-lactamase mutant M182N

ID or keywords:

Entry

Database: PDB / ID: 6b2n

Title

Crystal structure of TEM-1 beta-lactamase mutant M182N

Components

Beta-lactamase TEM

Keywords

HYDROLASE / Antibiotic resistance / beta-lactamase

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Jimah, J.R. / Tolia, N.H.

Citation

Journal: ACS Cent Sci / Year: 2017
Title: Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models.
Authors: Zimmerman, M.I. / Hart, K.M. / Sibbald, C.A. / Frederick, T.E. / Jimah, J.R. / Knoverek, C.R. / Tolia, N.H. / Bowman, G.R.

History

Deposition	Sep 20, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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	6b2n.cif.gz	550.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6b2n.ent.gz	463.5 KB	Display	PDB format
PDBx/mmJSON format	6b2n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6b2n_validation.pdf.gz	467.7 KB	Display	wwPDB validaton report
Full document	6b2n_full_validation.pdf.gz	476.2 KB	Display
Data in XML	6b2n_validation.xml.gz	37.8 KB	Display
Data in CIF	6b2n_validation.cif.gz	51.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/6b2n ftp://data.pdbj.org/pub/pdb/validation_reports/b2/6b2n	HTTPS FTP

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Related structure data

Related structure data	1jwpS S: Starting model for refinement
Similar structure data	3jyi-3 5hvi-3 5kpu-1 5i63-1 3jyi-2 1li0-d 1jwv-d 1zg4-d 6ayk-2 4oqg-2 1htz-4 5iq8-4 4ibx-1 1erm-d 5hw5-4 5hw1-1 1xpb-d 4ibr-d 4oqg-6 3jyi-5 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

1jwpS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#164 - Aug 2013 Serotonin Receptor similarity (6) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase TEM

B: Beta-lactamase TEM

C: Beta-lactamase TEM

D: Beta-lactamase TEM

hetero molecules

116 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase TEM

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

2

B: Beta-lactamase TEM

hetero molecules

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

3

C: Beta-lactamase TEM

hetero molecules

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

4

D: Beta-lactamase TEM

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.910, 49.660, 122.160
Angle α, β, γ (deg.)	90.00, 90.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 Mass: 28924.900 Da / Num. of mol.: 4 / Fragment: UNP residues 24-286 / Mutation: M182N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.15 Å³/Da / Density % sol: 42.75 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.1 M sodium phosphate dibasic/citric acid, pH 4.2, 0.1 M lithium sulfate, 20% PEG1000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 3, 2017
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. obs: 66091 / % possible obs: 98.6 % / Redundancy: 3.52 % / R_sym value: 0.099 / Net I/σ(I): 8.95
Reflection shell	Highest resolution: 2 Å / R_sym value: 0.506

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1JWP

1jwp

Resolution: 2→19.767 Å / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 31.92 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2828	1873	2.84 %
R_work	0.2307	-	-
obs	0.2347	66017	98.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→19.767 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7998	0	20	189	8207

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8138
X-RAY DIFFRACTION	f_angle_d	0.582	11009
X-RAY DIFFRACTION	f_dihedral_angle_d	15.186	4972
X-RAY DIFFRACTION	f_chiral_restr	0.039	1271
X-RAY DIFFRACTION	f_plane_restr	0.003	1420

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 (%)
2.0001-2.0541	0.3346	142	0.2958	4838	X-RAY DIFFRACTION	95
2.0541-2.1144	0.3027	142	0.2847	4882	X-RAY DIFFRACTION	96
2.1144-2.1825	0.3479	143	0.2731	4867	X-RAY DIFFRACTION	95
2.1825-2.2604	0.3431	142	0.278	4851	X-RAY DIFFRACTION	95
2.2604-2.3507	0.3224	144	0.267	4901	X-RAY DIFFRACTION	96
2.3507-2.4573	0.2949	139	0.2562	4908	X-RAY DIFFRACTION	96
2.4573-2.5865	0.2619	145	0.258	4917	X-RAY DIFFRACTION	96
2.5865-2.7479	0.3015	139	0.2542	4903	X-RAY DIFFRACTION	96
2.7479-2.9591	0.3201	142	0.2454	4926	X-RAY DIFFRACTION	96
2.9591-3.2551	0.3096	143	0.232	4983	X-RAY DIFFRACTION	97
3.2551-3.7219	0.2426	146	0.2017	4980	X-RAY DIFFRACTION	96
3.7219-4.6735	0.2398	140	0.171	5007	X-RAY DIFFRACTION	96
4.6735-17.178	0.2857	153	0.2339	5153	X-RAY DIFFRACTION	96

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	0.002	0.0068	-0.0012	0.0237	-0.0004	0.0067	0.0106	0.0028	0.009	-0.0215	0.0112	-0.0086	-0.0031	0.0052	0.0302	0.2136	-0.039	-0.0392	0.0268	0.0176	0.0651	-12.8234	21.7874	-53.7288
2	0.0002	0.001	0.0047	0.0027	-0.0079	0.0152	-0.0006	-0.009	-0.0162	-0.0095	0.0035	-0.0051	0.036	0.0082	0.001	0.3178	-0.0055	-0.0489	-0.0467	0.0598	-0.0078	-22.4699	0.6705	-49.2017
3	0.0023	-0.0024	0.0027	0.0078	-0.0072	0.0081	0.0025	0.005	-0.0034	-0.0044	-0.0016	0.0042	0.0074	-0.0039	-0.0005	0.2199	-0.0148	-0.0359	0.0196	-0.0356	-0.0046	-32.1324	-7.4982	-65.3949
4	0.0024	0.0007	-0.0008	0.0027	-0.0011	0.0014	-0.0028	0.0026	-0.0088	-0.0019	-0.0013	0.002	0.0029	0.0021	0.0003	0.2044	0.0473	-0.0254	0.0433	-0.0123	0.0781	-23.309	-6.4488	-59.4593
5	0.0033	0.0068	0.0047	0.0078	0.0036	0.0006	-0.0054	0.0234	0.0116	-0.0145	-0.0198	-0.0035	-0.0046	0.0107	-0.0581	0.4106	-0.0133	-0.0637	-0.0743	-0.0735	-0.0101	-22.5584	2.8436	-50.1793
6	0.0059	-0.0065	0.0021	0.0084	-0.0022	0.0014	0.0043	0.0016	-0.001	-0.0009	0.0026	0.0002	0.0025	-0.0021	0.0051	0.1949	-0.0029	-0.0129	0.0247	0.0011	0.0171	-19.4662	8.1137	-60.0662
7	0.0104	-0.0107	0.021	0.0086	-0.0202	0.0473	0.0246	0.0107	0.0119	-0.0022	0.0079	-0.0229	0.0009	0.0012	0.0755	0.2146	-0.007	0.0275	0.0041	-0.0419	-0.0237	-12.4854	13.5837	-58.0296
8	0.0002	-0.0003	0.0006	0.0005	-0.0002	-0	0.0026	0.0053	0.0008	0.0079	-0.0046	0.0042	-0.0039	-0.0004	0	0.3406	0.022	-0.0241	0.1294	0.0451	0.2759	-29.7838	0.2241	-22.8938
9	-0.0023	0.0026	0.0018	0.0106	0.0039	0.0064	0.0024	-0.0005	-0.0018	0.0415	-0.0047	0.0154	0.038	-0.004	0.0062	0.5341	0.0217	-0.1269	-0.0897	0.1372	0.025	-16.6667	-25.6757	-26.1824
10	0.0032	0.0008	0.0036	0.0049	0.0017	0.0026	0.0087	0.0014	0.002	-0.0045	-0.0053	-0.0051	0.0075	0.0009	0.0069	0.2619	-0.0093	-0.0921	0.034	0.0459	0.0756	-10.2928	-15.0559	-29.969
11	0.0014	-0.0009	-0.001	0.0045	0.0003	0.0028	-0.0028	0.0009	-0.002	-0.0033	-0.0014	0.0052	-0.0016	-0.0018	-0.0071	0.2592	0.0015	-0.0698	0.0354	0.0085	0.0473	-27.6111	-26.4885	-31.6602
12	-0.0001	-0.0002	-0.0001	-0	-0.0001	-0.0001	-0.0008	0.001	0.0132	0.0021	0.0017	0.0088	-0.0015	-0.005	-0.0051	0.2147	0.0368	0.0267	0.0771	0.0233	0.0976	-31.7662	-19.8035	-17.658
13	-0.0002	0.0009	0.0002	0.0023	-0.0025	0.001	0.0005	-0.0067	-0.0057	-0.0135	0.0012	0.0212	0.0039	-0.0035	-0.0039	0.2477	-0.0016	0.0133	0.0925	0.0709	0.1252	-26.8431	-16.9983	-21.3255
14	-0.0001	-0	0.0001	0	-0.0005	0.0005	0.0003	-0.002	0.0066	-0.0013	0.0057	0.0036	-0.0019	-0.0073	0	0.2267	-0.0353	-0.006	0.1105	0.0313	0.1968	-23.1319	-10.0487	-21.6252
15	0.0002	-0.0001	-0.0004	-0	0.0003	0.0013	0.003	0.0021	0.0013	-0.0002	-0.001	0.0042	-0.0025	-0.0042	-0.0024	0.1623	0.0396	0.0378	0.0801	0.062	0.1606	-32.2739	-7.1963	-18.386
16	0.0004	0.0001	-0.0002	0.0001	0.0002	0.0001	0.0052	-0.0018	-0.0027	-0.0097	0.0075	0.0018	-0.0011	-0.0038	-0	0.182	-0.061	-0.0104	0.0642	0.0048	0.1133	-28.7143	-29.3519	5.1857
17	0.0478	-0.0229	-0.0199	0.0193	0.0006	0.0224	0.009	-0.0009	0.0061	-0.0039	0.005	0.0014	0.0068	-0.008	0.0272	0.1321	0.0036	0.0382	0.018	-0.0112	0.0228	-29.3801	-19.1785	14.2611
18	0.0149	0.0025	-0.0049	0.0138	0.0004	0.0275	0.0018	-0.0009	-0.002	0.0058	0.0076	0.004	-0.0109	0.001	0.0264	0.1892	0.0115	0.046	-0.0106	-0.0006	0.0177	-17.1422	-8.0898	12.5926
19	-0.0028	-0.0003	0.0005	0.0037	-0.0008	0.0213	0.0153	0.0037	0.0171	-0.0154	-0.01	0.005	-0.0217	-0.0001	-0.001	0.4194	-0.0118	0.0694	-0.0427	0.0526	0.0033	-11.4085	2.6259	5.1148
20	0.0043	0.0075	-0.0067	0.0118	-0.0093	0.0074	-0.0002	0.0027	-0.0028	0.0095	-0.0144	-0.0104	0.0096	0.0044	-0.0291	0.2574	-0.0144	0.0715	0.0028	-0.0027	0.0008	-13.7272	-12.6012	13.4052
21	-0.0024	-0.0006	0.0008	0.0026	0.0018	0.0231	-0.006	0.0086	-0.0086	-0.0034	0.0024	0.006	-0.0174	-0.0068	-0.0158	0.241	0.0179	0.0251	-0.0099	0.0331	-0.0011	-26.7703	-8.8751	5.4231
22	0.0005	0.0003	-0.0004	-0.0003	0.0003	0.0002	0.0055	0.0051	-0.0082	0.0035	0.0018	-0.0018	0.0068	-0.0042	0.0018	0.2244	-0.066	-0.041	0.1233	-0.0112	0.0671	-29.9605	-21.2323	-0.0104
23	-0.0011	-0.0001	-0.0011	0.002	-0.0028	0.0001	-0.0073	-0.0053	-0.0039	-0.0025	0.0011	0.0014	0.0007	-0.0078	-0.0163	0.221	-0.0257	0.0206	-0.0063	0.0485	0.0182	14.0997	-22.8429	-33.037
24	-0.0019	-0.0001	-0.0021	0.0053	0.0001	0.0018	-0.0001	-0.0004	0.009	0.0197	-0.0008	-0.0009	-0.0168	0.0039	-0.0007	0.2574	0.0224	0.0771	-0.0521	0.0739	-0.0124	27.9202	4.4911	-38.7718
25	0.0024	0.0039	0.0048	0.0053	0.0041	0.0037	0.0023	0.0037	-0.0028	-0.0098	-0.0098	-0.0066	-0.0047	0	-0.0148	0.18	-0.0039	0.0595	-0.0274	0.0088	-0.0125	26.6897	-0.6718	-33.3188
26	0.0014	0.0017	-0.0033	0.0016	-0.0024	0.0051	0.0077	0.0037	0.0012	0.0032	-0.0076	-0.0014	0.0037	0.0031	0.0081	0.1907	-0	0.0938	0.0466	0.0304	0.1088	31.2318	-13.7028	-31.2847
27	0.0023	0.0009	0.0044	0.0005	0.0019	0.0085	-0.0066	0.0006	-0.0001	0.0008	-0.0029	0.0067	0.0046	-0.0028	-0.0235	0.1464	0.0023	0.0256	0.0072	0.0318	-0.0183	16.0912	-10.7428	-26.9672
28	0.0016	0.0001	0.0003	0.0018	-0.001	0.0005	0.0001	0.0012	0.0054	-0.0007	-0.005	0.0047	0.0026	0.0012	-0.004	0.2081	-0.0068	0.0233	0.0366	0.0625	0.0884	12.3021	1.6968	-32.0213
29	0.0006	-0.0001	-0.002	0.0171	-0.0035	0.0061	0.015	-0.0026	-0.0074	-0.0126	0.0079	0.016	0.0024	-0.0053	0.0066	0.2009	-0.0411	0.0151	0.0421	0.0129	0.0662	9.4499	-11.262	-45.6602
30	0.0002	-0.0015	-0.0004	0.0049	-0.0017	0.0026	0.0056	0.0005	0.0005	0.0038	0.009	0.0103	0.0087	-0.0082	0.0115	0.137	-0.0054	0.024	0.0101	0.042	0.0662	16.9662	-12.0866	-40.9149
31	0.0011	0.0028	-0.0037	0.0106	-0.0106	0.0092	0.0157	0.001	0.0104	0.0046	0.0149	0.0209	-0.0071	-0.0099	0.016	0.1809	-0.0247	-0.0118	0.0448	0.0294	0.0813	13.1149	-16.2645	-37.8889
32	0.0001	-0.0004	-0.0005	0.0001	0.0001	-0.0002	0.0123	-0.0053	-0.003	-0.0174	0.0014	0.0103	0.0076	-0.0096	-0	0.3688	-0.0166	-0.0296	0.134	0.0623	0.1553	10.8924	-21.6913	-44.1523

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 26 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 98 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 118 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 119 through 131 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 132 through 229 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 230 through 244 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 245 through 288 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 40 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 41 through 155 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 156 through 182 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 183 through 212 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 213 through 234 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 235 through 256 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 257 through 271 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 272 through 288 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 26 through 40 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 42 through 60 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 61 through 86 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 87 through 155 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 156 through 195 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 196 through 269 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 270 through 288 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 26 through 70 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 71 through 118 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 119 through 155 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 156 through 179 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 180 through 195 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 196 through 213 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 214 through 229 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 230 through 250 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 251 through 269 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 270 through 288 )

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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

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+About Yorodumi

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-Aug 12, 2020. Covid-19 info

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Download

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Validation report

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi