PDB-7u4b: Ampicillin-CTX-M-15

ID or keywords:

Entry

Database: PDB / ID: 7u4b

Title

Ampicillin-CTX-M-15

Components

Beta-lactamase

Keywords

HYDROLASE / antibiotics / complex / b-lactamase / Ampicillin / CTX-M-15 / STRUCTURAL PROTEIN

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.92 Å

Authors

Ahmadvand, P. / Kang, C.H.

Funding support

United States, 1items

Citation

Journal: Int J Mol Sci / Year: 2022
Title: Characterization of Interactions between CTX-M-15 and Clavulanic Acid, Desfuroylceftiofur, Ceftiofur, Ampicillin, and Nitrocefin.
Authors: Ahmadvand, P. / Avillan, J.J. / Lewis, J.A. / Call, D.R. / Kang, C.

History

Deposition	Feb 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7u4b.cif.gz	315.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7u4b.ent.gz	256.2 KB	Display	PDB format
PDBx/mmJSON format	7u4b.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/u4/7u4b ftp://data.pdbj.org/pub/pdb/validation_reports/u4/7u4b	HTTPS FTP

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Related structure data

Related structure data	7u48C 7u49C 7u57C 4hbtS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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
Related items in Molecule of the Month	#164 - Aug 2013 Serotonin Receptor similarity (5) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

hetero molecules

94.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase

hetero molecules

defined by author
Evidence: isothermal titration calorimetry
31.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-lactamase

hetero molecules

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

3

C: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	170.955, 50.939, 106.597
Angle α, β, γ (deg.)	90.000, 113.450, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-431- HOH

#1: Protein	Beta-lactamase Mass: 31075.451 Da / Num. of mol.: 3 / Mutation: A48P, Q49L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaCTX-M-15 / Production host: Escherichia coli (E. coli) / References: UniProt: C7S9T0, beta-lactamase
#2: Chemical	ChemComp-NW3 / (2S,4S)-2-[(1S)-1-{[(2S)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid Mass: 351.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₂₁N₃O₄S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.29 Å³/Da / Density % sol: 46.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 300 mM Ammonium sulfate, 30% PEG 4000

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 57183 / % possible obs: 94.1 % / Redundancy: 6 % / B_iso Wilson estimate: 27.2 Å² / R_merge(I) obs: 0.119 / R_pim(I) all: 0.05 / R_rim(I) all: 0.129 / Χ²: 1.584 / Net I/σ(I): 5.3 / Num. measured all: 775061

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.5-1.53	2.4	1.172	2998	0.368	0.766	1.412	0.445	44.3
1.53-1.55	2.8	1.208	4326	0.485	0.726	1	0.437	63.6
1.55-1.58	3.6	1.211	5745	0.515	0.656	1	0.436	84.6
1.58-1.62	4.4	1.132	6436	0.579	0.565	1.272	0.446	94.9
1.62-1.65	5.9	1.01	6760	0.775	0.44	1	0.46	99.2
1.65-1.69	6.3	0.902	6733	0.828	0.383	0.982	0.467	99.5
1.69-1.73	6.3	0.712	6738	0.87	0.304	0.776	0.481	99.4
1.73-1.78	6.1	0.602	6774	0.897	0.262	0.658	0.5	99.4
1.78-1.83	6.5	0.474	6787	0.93	0.198	0.514	0.535	99.6
1.83-1.89	6.3	0.379	6788	0.951	0.162	0.413	0.587	99.4
1.89-1.96	6.7	0.45	6726	0.942	0.184	0.487	2.097	99.5
1.96-2.04	6.5	0.237	6828	0.979	0.099	0.258	0.847	99.6
2.04-2.13	6.3	0.191	6793	0.984	0.082	0.208	0.985	99.4
2.13-2.24	6.6	0.183	6786	0.984	0.076	0.199	1.486	99.8
2.24-2.38	6.6	0.194	6819	0.968	0.082	0.211	3.277	99.9
2.38-2.56	6.8	0.125	6857	0.99	0.051	0.135	1.879	100
2.56-2.82	6.6	0.112	6865	0.992	0.047	0.121	2.137	100
2.82-3.23	6.8	0.095	6873	0.994	0.039	0.103	2.8	100
3.23-4.07	6.7	0.083	6935	0.994	0.035	0.09	3.859	100
4.07-50	6.6	0.078	7084	0.989	0.033	0.085	3.641	100

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HBT

4hbt

Resolution: 1.92→48.9 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2699	1791	3.16 %
R_work	0.2167	54883	-
obs	0.2184	56674	87.46 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 129.46 Å² / B_iso mean: 46.0985 Å² / B_iso min: 19.33 Å²

Refinement step

Cycle: final / Resolution: 1.92→48.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5844	0	77	251	6172
B_iso mean	-	-	57.97	45.48	-
Num. residues	-	-	-	-	780

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.92-1.97	0.4475	71	0.3701	2094	2165	44
1.97-2.03	0.3982	87	0.34	2710	2797	57
2.03-2.1	0.3698	112	0.3241	3413	3525	72
2.1-2.17	0.3159	130	0.3152	3994	4124	83
2.17-2.26	0.3627	144	0.2915	4378	4522	92
2.26-2.36	0.3024	149	0.2711	4649	4798	97
2.36-2.48	0.3041	155	0.2449	4684	4839	97
2.48-2.64	0.307	153	0.2371	4730	4883	98
2.64-2.84	0.2728	157	0.2341	4756	4913	98
2.84-3.13	0.269	154	0.2127	4786	4940	99
3.13-3.58	0.2488	158	0.1958	4844	5002	100
3.58-4.51	0.2064	159	0.1661	4856	5015	100
4.51-48.9	0.2534	162	0.1793	4989	5151	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	2.2991	0.2057	-1.3913	1.2833	0.803	2.6787	0.062	-0.3744	-0.2454	0.2532	-0.2106	-0.1398	0.1073	0.3311	0.2515	0.3349	-0.3341	0.0166	0.8603	0.3728	0.3441	-64.348	-14.895	31.151
2	1.2068	0.1076	-1.0623	0.8374	0.0935	1.1007	0.3677	-0.1883	0.1912	-0.0286	-0.242	-0.2248	-0.4904	0.0864	-0.1778	0.5669	-0.4903	0.1986	1.1523	0.1959	0.1702	-70.196	1.179	31.901
3	1.2458	0.0557	-1.2092	1.7147	-1.0818	4.8408	0.1546	-0.0208	0.0351	0.0557	-0.1312	-0.0011	-0.4274	0.0176	-0.2339	0.4353	-0.3591	0.1265	0.9514	0.0602	0.2399	-75.54	-2.328	36.079
4	1.4946	-1.3421	-0.9121	2.2353	-0.8353	5.6947	0.2949	0.0954	0.1102	0.1406	-0.2688	0.0174	-1.0672	-0.0871	-0.077	0.852	-0.3244	0.2492	0.9216	-0.0556	0.3142	-78.342	8.104	31.354
5	5.7192	-2.0571	-0.5694	4.5613	0.7022	0.4586	-0.2908	0.8762	0.963	-0.8459	0.2033	-0.1956	-0.3392	0.0952	0.0864	0.5307	-0.1621	-0.0486	0.317	0.1101	0.4011	-37.223	22.449	22.293
6	2.2626	0.8639	-0.0542	1.0282	0.2882	1.781	-0.3994	-1.1616	-0.6101	0.1382	-0.012	0.004	0.3303	-0.2606	0.2142	0.475	0.187	0.1806	0.5842	0.1882	0.3374	-48.205	3.914	45.224
7	7.1422	2.0542	-3.779	1.3127	0.6416	6.1385	-0.5232	-1.4618	-0.3342	0.2972	0.1855	-0.1281	0.3577	0.3442	0.2985	0.3434	0.2089	0.0131	0.6129	0.0343	0.314	-33.42	12.03	45.623
8	3.7292	0.2615	0.6204	0.7757	-0.0184	1.9773	-0.4694	-0.3361	-0.1224	0.066	0.2582	0.0429	0.1468	0.0044	0.1795	0.3475	0.0499	0.0784	0.1522	-0.027	0.2159	-41.061	11.627	32.832
9	3.4715	-0.1511	0.2191	3.3916	0.6893	2.9539	-0.4542	0.5666	-0.1946	-0.1279	0.1809	0.0827	0.0919	0.2169	0.2554	0.319	-0.0491	0.0347	0.2021	-0.0121	0.2822	-38.921	10.607	21.242
10	5.5217	-0.9376	-1.0618	6.3254	-0.5968	2.0065	-0.2246	0.738	0.5089	-0.0834	-0.2082	0.2081	-0.3643	-0.3164	0.4277	0.3279	0.0239	-0.1155	0.2344	0.0567	0.3289	-48.761	21.646	23.121
11	1.7131	-1.5004	0.3412	3.2998	0.9089	1.5821	-0.2694	-0.4359	-0.0761	0.6508	0.061	0.0378	0.5471	1.0662	0.2042	0.5393	0.1993	0.1144	0.9697	-0.031	0.3138	-13.079	-8.241	20.919
12	1.5756	-0.7984	-0.0658	2.3017	0.0812	3.7364	0.041	0.2744	-0.0301	-0.0691	-0.3006	0.2751	-0.049	0.0126	0.249	0.2795	-0.0189	0.0684	0.5596	-0.1913	0.3128	-26.203	2.085	-5.077
13	2.6561	-0.3707	0.0667	2.3972	0.3086	5.581	-0.0525	0.3636	-0.3083	-0.1921	-0.2494	0.1404	0.8521	0.0737	0.3184	0.6417	0.0317	0.1419	0.6828	-0.261	0.4049	-23.424	-13.66	-13.922
14	0.919	-0.2817	-0.6687	1.4768	-0.0368	3.0577	0.1215	0.1306	-0.1297	0.1172	-0.275	0.1515	0.2355	0.6035	0.1661	0.303	0.0229	0.0697	0.6047	-0.1654	0.2943	-20.842	-4.251	3.917
15	2.6303	0.9712	1.633	3.7486	-0.9222	1.7043	0.0071	-0.4317	-0.344	0.4971	0.0426	0.1716	0.7368	0.4989	-0.0221	0.5785	0.168	0.1067	0.6493	-0.0102	0.3016	-19.179	-13.356	16.693
16	0.9066	0.4982	-0.0786	2.5881	-0.4082	0.0636	0.2179	-0.1495	0.211	0.9411	-0.0375	0.632	-0.7074	-0.827	-0.1821	0.765	-0.0531	0.1848	1.2174	-0.0162	0.3622	-86.137	4.707	34.967
17	0.5725	-0.732	-0.8589	1.1107	0.6535	3.0951	0.2301	0.2035	-0.261	0.1304	-0.3799	0.2297	-0.2479	-0.6891	0.1573	0.3698	-0.2138	0.1156	1.057	0.0446	0.2978	-84.225	-5.619	31.535
18	0.9299	-0.7301	-0.8795	1.4718	0.7202	1.9811	0.2668	-0.0339	-0.0768	-0.1651	-0.3461	-0.1647	-0.221	-0.1323	0.0455	0.3467	-0.1114	0.028	0.7465	0.2492	0.3563	-61.513	-12.627	16.79
19	1.8355	-0.4745	-1.1053	1.459	1.008	2.7101	0.4049	0.0541	0.0433	-0.0459	-0.4321	-0.1306	-0.4171	-0.2657	0.0053	0.376	-0.0665	0.0361	0.7146	0.1734	0.2709	-69.458	-6.779	17.579

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN C AND RESID 195:212 )	C	195 - 212
2	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 213:250 )	C	213 - 250
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 251:265 )	C	251 - 265
4	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 266:287 )	C	266 - 287
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 28:68 )	A	28 - 68
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 69:142 )	A	69 - 142
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 143:155 )	A	143 - 155
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 156:250 )	A	156 - 250
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 251:264 )	A	251 - 264
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 265:287 )	A	265 - 287
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 28:68 )	B	28 - 68
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 69:96 )	B	69 - 96
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 97:115 )	B	97 - 115
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 116:250 )	B	116 - 250
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 251:287 )	B	251 - 287
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 28:51 )	C	28 - 51
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 52:68 )	C	52 - 68
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 69:101 )	C	69 - 101
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 102:194 )	C	102 - 194

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