PDB-5iq8: Crystal structure of TEM1 beta-lactamase mutant A224C/G283C disulfide

ID or keywords:

Entry

Database: PDB / ID: 5iq8

Title

Crystal structure of TEM1 beta-lactamase mutant A224C/G283C disulfide

Components

Beta-lactamase TEM

Keywords

HYDROLASE / Enzyme / disulfide

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.06 Å

Authors

Roose, B.W. / Dmochowski, I.J.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01-GM097478	United States
Department of Defense Lung Cancer Research Program	W81XWH-14-1-0424	United States

Citation

Journal: To Be Published
Title: Structure of TEM1 beta-lactamase
Authors: Roose, B.W. / Wang, Y. / Dmochowski, I.J.

History

Deposition	Mar 10, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 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
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5iq8.cif.gz	408.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5iq8.ent.gz	336.3 KB	Display	PDB format
PDBx/mmJSON format	5iq8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/5iq8 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iq8	HTTPS FTP

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Related structure data

Related structure data	5hw5C 5hviS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vnk-1 4ibx-5 6yc8-d 3a2h-2 5kkf-4 2phg-d 2vni-d 6apa-1 3g35-2 7kl5-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) 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

5hw5C

5hviS

S: Starting model for refinement

C: citing same article (ref.)

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

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

1

A: Beta-lactamase TEM

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

2

B: Beta-lactamase TEM

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

3

C: Beta-lactamase TEM

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

4

D: Beta-lactamase TEM

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

Unit cell

Length a, b, c (Å)	60.858, 84.705, 96.344
Angle α, β, γ (deg.)	90.00, 90.00, 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: 28990.061 Da / Num. of mol.: 4 / Mutation: M180T, A222C, G279C 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 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.14 Å³/Da / Density % sol: 42.56 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium tartrate dibasic (pH 7.0), 20% (w/v) PEG 3350 PH range: 7.0 - 7.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection twin	Operator: h,-k,-l / Fraction: 0.48
Reflection	Resolution: 2.06→63.61 Å / Num. obs: 59865 / % possible obs: 99 % / Redundancy: 2.5 % / R_merge(I) obs: 0.13 / Net I/σ(I): 5.6
Reflection shell	Resolution: 2.06→2.11 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.555 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
Aimless	0.5.17	data scaling
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HVI

5hvi

Resolution: 2.06→63.61 Å / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.33

	R_factor	Num. reflection	% reflection
R_free	0.241	5933	5.04 %
R_work	0.191	-	-
obs	0.197	59841	98.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 14.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→63.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8054	0	0	777	8831

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8210
X-RAY DIFFRACTION	f_angle_d	0.597	11133
X-RAY DIFFRACTION	f_dihedral_angle_d	11.734	3059
X-RAY DIFFRACTION	f_chiral_restr	0.023	1294
X-RAY DIFFRACTION	f_plane_restr	0.003	1451

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 (%)
2.0601-2.0956	0.3394	296	0.2548	5638	X-RAY DIFFRACTION	95
2.0956-2.1336	0.3027	274	0.2397	5576	X-RAY DIFFRACTION	95
2.1336-2.1746	0.2981	278	0.2356	5688	X-RAY DIFFRACTION	95
2.1746-2.219	0.2788	326	0.2287	5611	X-RAY DIFFRACTION	94
2.219-2.2671	0.2661	328	0.2223	5555	X-RAY DIFFRACTION	94
2.2671-2.3198	0.2786	357	0.2204	5566	X-RAY DIFFRACTION	94
2.3198-2.3777	0.2686	278	0.2205	5616	X-RAY DIFFRACTION	95
2.3777-2.4419	0.2962	277	0.2158	5612	X-RAY DIFFRACTION	95
2.4419-2.5136	0.2461	210	0.2122	5689	X-RAY DIFFRACTION	96
2.5136-2.5946	0.2712	296	0.2023	5640	X-RAY DIFFRACTION	95
2.5946-2.6871	0.2479	359	0.2011	5564	X-RAY DIFFRACTION	93
2.6871-2.7944	0.2474	355	0.1994	5537	X-RAY DIFFRACTION	93
2.7944-2.9211	0.2588	280	0.1977	5611	X-RAY DIFFRACTION	94
2.9211-3.0746	0.2482	272	0.1888	5568	X-RAY DIFFRACTION	94
3.0746-3.2664	0.2331	288	0.1842	5569	X-RAY DIFFRACTION	94
3.2664-3.5173	0.2255	283	0.1665	5542	X-RAY DIFFRACTION	93
3.5173-3.8688	0.1918	282	0.1622	5576	X-RAY DIFFRACTION	93
3.8688-4.423	0.1955	297	0.1573	5526	X-RAY DIFFRACTION	93
4.423-5.5513	0.1816	218	0.1582	5577	X-RAY DIFFRACTION	94
5.5513-19.5858	0.2023	333	0.1875	5436	X-RAY DIFFRACTION	91

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	0.6117	-0.1414	-0.2189	1.1385	-0.167	1.1359	0.0759	-0.0516	-0.1209	0.0801	-0.1438	-0.073	0.2134	0.1087	0.0601	0.1003	-0.0013	0.0101	0.0643	0.0102	0.1197	19.3053	-23.3191	11.1031
2	0.1923	-0.0864	0.042	0.1777	-0.0638	0.1707	0.0401	0.0577	0.1206	-0.0082	-0.0112	0.0046	-0.0933	0.0344	0.0735	0.1393	-0.0006	0.0271	0.0261	0.0341	0.068	17.4475	-5.97	-15.4853
3	0.3	-0.0019	-0.2405	0.4577	-0.0233	0.4404	0.0633	-0.0009	0.0945	0.0941	0.0478	-0.0894	-0.0658	-0.0343	-0.0568	0.129	0.0087	0.022	0.0312	0.0102	0.0892	14.8328	-5.9789	-3.7181
4	0.0175	0.0222	0.0135	0.1162	0.0506	0.0228	-0.0164	-0	-0.023	0.0022	0.0131	0.0212	0.0129	-0.0085	0.0506	0.1471	-0.0108	0.0104	-0.0047	-0.0364	0.0717	10.1695	-20.1281	-6.3154
5	1.8385	2.2117	-0.2764	3.6345	-0.7047	0.8002	0.1118	-0.1028	-0.3973	0.0757	-0.2044	-0.4538	0.049	0.1783	0.1158	0.0653	0.001	0.0023	0.1492	-0.0014	0.1341	27.2743	-26.1782	-5.2879
6	0.5459	-0.5794	-0.5795	0.9198	0.7316	1.8084	-0.0241	-0.1756	0.0541	-0.0623	0.1306	-0.2148	-0.2639	0.4868	-0.1256	0.1144	-0.0281	0.0155	0.2561	0.0283	0.0813	23.2273	-17.844	-0.4151
7	2.0359	-0.2491	-0.1889	0.6009	-0.6705	0.9277	0.0054	-0.1811	0.0385	-0.0318	-0.0908	0.044	0.0798	-0.0528	0.0872	0.0651	0.0067	-0.0117	0.0793	0.0439	0.0436	22.0452	-22.5275	3.2443
8	2.8347	1.1478	0.4194	1.4975	0.9696	1.1943	0.1108	-0.1612	-0.0498	0.0672	0.0827	-0.0945	-0.0733	0.2242	-0.1399	0.1848	-0.0252	0.0236	0.1692	0.0204	0.0657	28.7247	-26.6347	5.9445
9	2.6475	-0.6172	0.5587	2.6196	-0.4759	2.2413	-0.0674	0.1782	-0.0766	-0.2315	-0.0767	0.1064	0.0783	0.0012	0.114	0.0877	-0.0105	0.0102	0.1074	0.0029	0.0338	-8.3669	-24.401	8.4189
10	0.5081	0.2525	-0.49	0.7428	0.0106	1.0094	-0.0828	-0.0899	-0.1672	-0.0137	-0.0748	0.0006	0.1219	0.0262	0.0973	0.0713	-0.0415	0.0066	0.1002	0.0057	0.1002	1.2784	-20.9469	12.2102
11	0.127	0.1046	0.0363	0.0896	0.0355	0.1383	0.003	-0.0199	0.0415	0.0348	-0.0086	0.1356	-0.0936	-0.0327	0.0311	0.1497	0.0219	0.0223	-0.0148	-0.006	0.0831	-2.8943	-7.1373	36.4644
12	0.4981	-0.3264	-0.1496	1.0216	0.3391	0.1789	0.0796	0.0758	-0.0067	-0.1618	-0.0315	0.0032	-0.0525	-0.0054	-0.0524	0.1662	0.0134	-0.001	0.0197	0.0004	0.075	2.0315	-4.5548	22.2239
13	0.0697	-0.0706	-0.005	0.0704	0.0064	0.0679	-0.0079	0.0041	-0.0596	-0.0195	0.0293	0.0113	0.0382	-0.0066	0.0925	0.1644	-0.004	-0.0073	-0.01	0.0019	0.1119	-0.4586	-22.1673	27.1419
14	2.0714	0.8437	-0.296	0.5976	0.1968	1.1135	0.0648	0.1759	0.1704	-0.1906	-0.0129	0.0799	-0.2088	-0.1409	0.0171	0.1944	0.0264	-0.0384	0.072	-0.0165	0.1104	-6.7191	-21.5689	22.7926
15	2.1961	-0.1518	-0.3777	0.247	0.2709	0.3188	-0.0154	0.2658	0.2712	-0.0491	-0.0499	0.0315	-0.0556	0.0015	0.0541	0.1079	-0.0325	-0.0056	0.0625	0.0267	0.1094	-8.9891	-17.7718	14.4492
16	0.9018	-1.2875	-0.039	3.0755	0.1624	0.8313	0.0629	0.2387	-0.1173	-0.1527	-0.1415	0.2862	-0.1117	0.0741	0.0875	0.2102	-0.0319	-0.0208	0.14	-0.0367	0.0711	-13.9998	-26.2031	15.2897
17	1.0978	-0.2296	-0.0105	1.173	0.3485	1.1633	-0.0051	-0.2139	0.1505	-0.0289	0.0285	0.0179	-0.1366	0.1326	-0.0085	0.1142	-0.002	0.0036	0.1359	-0.0294	0.073	26.4457	-12.3282	59.1981
18	0.08	0.0344	-0.0401	0.3651	-0.0265	0.1689	0.0194	0.0201	-0.0148	-0.0514	0.0054	-0.0292	0.0616	0.0036	0.0266	0.1071	0.0099	-0.013	0.0029	-0.013	0.0768	33.7831	-26.9203	33.989
19	0.1057	-0.0077	0.0175	0.1953	0.04	0.0146	-0.0075	-0.0538	-0.0372	0.0667	0.0206	0.0313	0.0495	-0.0058	-0.0226	0.1422	0.0089	0.0006	-0.0218	0.0307	0.0872	28.2388	-30.424	41.1599
20	0.0964	-0.157	0.0149	1.0233	-1.781	4.0184	0.0062	-0.1063	0.0346	-0.0011	-0.0801	-0.116	-0.0821	0.3041	0.0526	0.0754	-0.0081	0.0016	0.1606	-0.0361	0.0576	35.6361	-16.6452	49.1364
21	0.0939	0.0372	0.0371	0.0933	-0.0441	0.0745	-0.0114	-0.0187	0.0949	0.0034	0.0258	0.0048	-0.0563	-0.0199	0.0817	0.1271	0.0058	0.032	-0.0099	-0.0133	0.1085	27.4701	-11.8338	39.0171
22	1.0429	-0.0156	0.3557	0.3164	0.4679	1.2305	-0.0033	-0.0905	-0.0578	0.0068	0.0868	0.1774	0.109	-0.0239	-0.0616	0.117	0.018	0.0329	0.0362	0.0069	0.1247	23.7451	-13.8589	46.2485
23	2.2526	0.3963	0.3133	1.0695	0.4049	0.964	-0.0442	-0.2362	-0.0753	0.1194	-0.1144	0.0093	0.1833	0.0617	0.1074	0.1073	0.0593	0.0137	0.1212	-0.0095	0.0599	21.6729	-17.5767	54.8942
24	3.8896	4.0529	0.0074	7.3094	-0.516	0.7185	-0.0617	-0.0216	0.1778	0.0532	0.188	0.359	0.1101	-0.2674	-0.1071	0.1248	-0.018	-0.0059	0.1319	0.0216	0.0897	16.8422	-8.8675	54.0507
25	0.2926	-0.0618	-0.0547	0.3119	-0.1504	0.0986	-0.0287	-0.0803	0.0529	0.0711	0.0419	0.0393	-0.0792	0.0248	0.0034	0.1323	-0.0256	-0.0132	0.0425	-0.0217	0.081	13.5425	26.7257	32.4347
26	0.4132	-0.1947	-0.2067	0.0918	0.1022	0.1678	-0.0042	0.0493	-0.301	0.0048	-0.0433	0.0467	0.1142	-0.0724	0.0285	0.2268	-0.0584	-0.0242	0.0646	-0.0193	0.1613	12.5773	10.3943	8.7624
27	0.4512	-0.1343	-0.1088	0.4207	-0.1222	0.5381	-0.0257	0.0118	0.0066	0.0023	0.0567	0.0382	0.09	-0.0836	-0.0334	0.1034	-0.0256	0.0097	0.0335	0.0009	0.0307	14.1846	19.4552	20.5966
28	1.6138	-0.1073	-0.1504	0.2906	0.414	1.3092	0.0432	-0.0313	-0.0011	0.1168	0.0456	0.1191	0.0226	-0.103	-0.0841	0.1042	0.0135	0.0301	0.0833	0.0171	0.0693	7.8007	27.2201	28.2039
29	1.3381	-0.0934	0.3165	1.5785	-0.7609	0.4218	0.0863	0.0492	-0.091	-0.1446	0.122	0.1333	0.0116	-0.0384	-0.0921	0.185	-0.0024	0.0094	0.1219	-0.0579	0.1165	1.705	33.3485	32.7935

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 26 THROUGH 68 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 69 THROUGH 118 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 119 THROUGH 179 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 180 THROUGH 212 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 213 THROUGH 229 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 230 THROUGH 251 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 252 THROUGH 271 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 272 THROUGH 290 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 26 THROUGH 50 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 51 THROUGH 68 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 69 THROUGH 131 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 132 THROUGH 179 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 180 THROUGH 229 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 230 THROUGH 258 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 259 THROUGH 271 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 272 THROUGH 290 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 26 THROUGH 68 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 69 THROUGH 98 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 99 THROUGH 179 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 180 THROUGH 195 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 196 THROUGH 229 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 230 THROUGH 258 )
23	X-RAY DIFFRACTION	23	CHAIN 'C' AND (RESID 259 THROUGH 271 )
24	X-RAY DIFFRACTION	24	CHAIN 'C' AND (RESID 272 THROUGH 290 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 26 THROUGH 86 )
26	X-RAY DIFFRACTION	26	CHAIN 'D' AND (RESID 87 THROUGH 106 )
27	X-RAY DIFFRACTION	27	CHAIN 'D' AND (RESID 107 THROUGH 229 )
28	X-RAY DIFFRACTION	28	CHAIN 'D' AND (RESID 230 THROUGH 271 )
29	X-RAY DIFFRACTION	29	CHAIN 'D' AND (RESID 272 THROUGH 290 )

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