PDB-4ebl: BlaC E166A Faropenem Acyl-Intermediate Complex

ID or keywords:

Entry

Database: PDB / ID: 4ebl

Title

BlaC E166A Faropenem Acyl-Intermediate Complex

Components

Beta-lactamase

Keywords

Hydrolase/Antibiotic / Ambler Class A beta-lactamase / beta-lactamase / serine hydrolase / esterase / Hydrolase-Antibiotic complex / Structural Genomics / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Mire, J.A. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: To be Published
Title: Faropenem is Effective Against Mycobacterium tuberculosis in vitro and in vivo
Authors: Mire, J.A. / Pai, P. / Siddiqi, N. / Russell, D.H. / Rubin, E.J. / Sacchettini, J.C.

History

Deposition	Mar 23, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2017	Group: Non-polymer description
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ebl.cif.gz	402.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ebl.ent.gz	331.9 KB	Display	PDB format
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Validation report

Summary document	4ebl_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4ebl_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4ebl_validation.xml.gz	49.4 KB	Display
Data in CIF	4ebl_validation.cif.gz	66.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eb/4ebl ftp://data.pdbj.org/pub/pdb/validation_reports/eb/4ebl	HTTPS FTP

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Related structure data

Related structure data	4ebnC 4ebpC 3vff 3vfh 4ebi PDB Unreleased entry 4ebm PDB Unreleased entry 4ebo PDB Unreleased entry C: citing same article (ref.)
Similar structure data	3iqa-d 2gdn-d 3ndg-d 6b5x-2 6b5y-4 3vfh-3 5eua-1 3vff-3 3vfh-4 3vff-2 4ebp-2 4ebn-4 3vfh-1 3vfh-2 6b6b-d 3nbl-d 4mez-1 3n7w-d 4ibx-5 3vff-4 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

4ebi
PDB Unreleased entry

4ebm
PDB Unreleased entry

4ebo
PDB Unreleased entry

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 (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

D: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

3

C: Beta-lactamase

hetero molecules

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

4

D: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.792, 96.946, 109.526
Angle α, β, γ (deg.)	90.00, 107.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase / Penicillinase Mass: 28214.689 Da / Num. of mol.: 4 / Mutation: E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-DGF / (2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid / FAROPENEM PRODUCT, BOUND FORM Mass: 287.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₇NO₅S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.53 Å³/Da / Density % sol: 65.12 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 120 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D

Detector

Detector: CCD

Radiation

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

Radiation wavelength

Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. all: 91346 / Num. obs: 89782 / % possible obs: 99.6 % / Observed criterion σ(I): 2.3 / Redundancy: 5.1 % / B_iso Wilson estimate: 29.65 Å² / R_merge(I) obs: 0.125 / Net I/σ(I): 16.1

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
2.1-2.15	4.5	2.3	4161	1	99.6
2.15-2.19	5.1	3.2	4484	1	92.7
2.19-2.23	5.1	3.7	4477	1	100
2.23-2.27	5.1	4.2	4467	1	100
2.27-2.32	5.1	5	4515	1	100

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-3000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→46.859 Å / SU ML: 0.24 / σ(F): 1.34 / σ(I): 2.3 / Phase error: 20.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2039	4471	4.99 %	random
R_work	0.1733	-	-	-
obs	0.1749	89613	98.17 %	-
all	-	91346	-	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.506 Å² / k_sol: 0.372 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.6371 Å²	-0 Å²	-3.8869 Å²
2-	-	-1.8125 Å²	0 Å²
3-	-	-	1.1754 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→46.859 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7874	0	78	428	8380

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	8104
X-RAY DIFFRACTION	f_angle_d	1.494	11083
X-RAY DIFFRACTION	f_dihedral_angle_d	13.776	2889
X-RAY DIFFRACTION	f_chiral_restr	0.093	1284
X-RAY DIFFRACTION	f_plane_restr	0.009	1455

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 (%)
2.1-2.1251	0.3333	80	0.2787	1384	X-RAY DIFFRACTION	49
2.1251-2.1501	0.2673	129	0.2323	2883	X-RAY DIFFRACTION	99
2.1501-2.1763	0.2823	146	0.2184	2853	X-RAY DIFFRACTION	100
2.1763-2.2039	0.2583	157	0.2119	2857	X-RAY DIFFRACTION	100
2.2039-2.2329	0.2628	153	0.2089	2882	X-RAY DIFFRACTION	100
2.2329-2.2634	0.2217	158	0.2068	2868	X-RAY DIFFRACTION	100
2.2634-2.2958	0.2619	132	0.1993	2897	X-RAY DIFFRACTION	100
2.2958-2.33	0.2436	140	0.2	2883	X-RAY DIFFRACTION	100
2.33-2.3664	0.2594	142	0.1886	2893	X-RAY DIFFRACTION	100
2.3664-2.4052	0.2415	144	0.1746	2856	X-RAY DIFFRACTION	100
2.4052-2.4467	0.2289	166	0.185	2888	X-RAY DIFFRACTION	100
2.4467-2.4912	0.2236	194	0.172	2829	X-RAY DIFFRACTION	100
2.4912-2.5391	0.2221	118	0.1731	2888	X-RAY DIFFRACTION	100
2.5391-2.5909	0.2126	153	0.1792	2863	X-RAY DIFFRACTION	100
2.5909-2.6473	0.2129	153	0.1796	2908	X-RAY DIFFRACTION	100
2.6473-2.7088	0.2153	148	0.1811	2919	X-RAY DIFFRACTION	100
2.7088-2.7766	0.1959	133	0.1767	2873	X-RAY DIFFRACTION	100
2.7766-2.8516	0.1998	140	0.1822	2889	X-RAY DIFFRACTION	100
2.8516-2.9355	0.2453	170	0.1886	2888	X-RAY DIFFRACTION	100
2.9355-3.0303	0.2059	150	0.1847	2907	X-RAY DIFFRACTION	100
3.0303-3.1386	0.2261	158	0.1757	2865	X-RAY DIFFRACTION	100
3.1386-3.2642	0.2	136	0.1758	2884	X-RAY DIFFRACTION	100
3.2642-3.4127	0.1945	152	0.1751	2919	X-RAY DIFFRACTION	100
3.4127-3.5926	0.1911	155	0.1607	2886	X-RAY DIFFRACTION	100
3.5926-3.8176	0.1778	160	0.1582	2873	X-RAY DIFFRACTION	100
3.8176-4.1122	0.1739	160	0.1514	2906	X-RAY DIFFRACTION	100
4.1122-4.5257	0.1478	154	0.1395	2909	X-RAY DIFFRACTION	100
4.5257-5.1798	0.1757	141	0.138	2931	X-RAY DIFFRACTION	100
5.1798-6.5233	0.2277	181	0.19	2908	X-RAY DIFFRACTION	100
6.5233-46.8707	0.1804	168	0.1772	2953	X-RAY DIFFRACTION	99

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	0.6526	0.0373	-0.155	0.4991	-0.4715	0.8126	-0.0418	0.2074	-0.1892	-0.2972	0.0372	-0.0843	0.0921	0.0551	-0.0012	0.1584	-0.0195	0.0099	0.1948	-0.0375	0.1908	28.4823	1.4176	-5.6321
2	0.8923	0.0295	-0.0462	0.8343	-0.1173	0.4569	0.063	-0.1974	0.2355	0.1327	-0.0104	-0.0645	-0.1739	0.07	0	0.2247	-0.0299	0.0041	0.2797	-0.0623	0.2505	31.2599	19.7935	19.7609
3	0.3143	0.372	0.1	0.4163	0.1382	0.4461	-0.0364	0.0916	0.1468	-0.1423	0.0133	0.0862	-0.0962	-0.1134	0	0.2412	-0.028	0.0104	0.2471	0.0158	0.3017	34.5584	20.8822	3.0137
4	0.678	0.032	-0.0785	0.9029	-0.1851	0.4992	-0.0213	0.015	-0.0648	-0.0137	0.0296	-0.0244	-0.0416	-0.0003	-0	0.1395	-0.0047	-0.0005	0.186	-0.0006	0.1933	29.279	3.6865	7.3535
5	0.4167	-0.3759	0.094	0.4121	0.1404	0.5467	0.0307	-0.0808	-0.3151	0.379	0.0677	-0.0545	0.0706	-0.0309	0.0013	0.3619	-0.0219	0.019	0.2309	0.0059	0.2124	10.0059	-1.9822	46.8285
6	0.2192	0.1985	0.38	0.7215	-0.3156	0.8387	-0.0733	0.0467	0.1948	0.1579	0.0445	0.0245	-0.2366	-0.0547	0.0068	0.1875	0.0384	0.0139	0.2494	-0.0236	0.2254	1.9099	8.5705	29.3506
7	0.7635	-0.0927	-0.6142	0.5043	-0.5298	1.0274	0.0584	-0.1569	0.2692	0.1632	0.0561	0.0288	-0.2019	0.1441	-0.0021	0.2095	0.0133	0.0125	0.1955	-0.0382	0.2371	6.0378	15.0253	22.016
8	0.3053	-0.1725	0.0366	0.9439	-0.5794	0.786	0.0416	-0.001	-0.0432	0.1296	0.0377	0.0471	0.0089	-0.0124	-0	0.2221	-0.0021	0.0063	0.195	-0.009	0.178	6.9756	-0.3918	32.9731
9	0.3984	0.0115	-0.313	0.2253	0.1783	0.3763	0.0443	0.1079	0.1898	-0.2006	-0.053	-0.1852	-0.0433	0.1057	-0.0002	0.1671	0.0246	0.0194	0.1672	0.0186	0.2089	26.5804	-21.3581	-3.0361
10	0.8347	-0.2607	-0.2326	1.3589	-0.1228	0.7196	0.0195	-0.0984	-0.1641	0.1481	0.0988	0.2408	0.2812	-0.0817	0.0266	0.2094	-0.0413	0.0204	0.2413	0.0329	0.2641	8.1049	-35.0366	14.982
11	0.634	0.0297	-0.5279	0.3953	0.2066	0.5407	-0.0297	-0.2361	-0.2282	0.1715	0.0505	-0.2566	0.4138	0.1885	0	0.3546	-0.0083	-0.0692	0.3015	-0.0155	0.3782	12.9164	-41.4808	3.6289
12	0.7175	-0.014	-0.2192	1.129	-0.3063	0.663	-0.0114	-0.0248	0.0616	-0.011	0.0224	0.0428	0.0546	0.0015	0	0.1233	0.006	0.0047	0.1654	-0.0167	0.1758	15.9402	-23.2048	6.3248
13	0.6098	-0.1232	-0.1415	0.4158	-0.1439	0.9174	-0.0352	-0.0688	0.1658	0.3386	0.1106	0.1299	-0.1887	-0.0806	0	0.3413	0.0121	0.0331	0.2084	0.0181	0.2197	10.5512	-24.8266	50.271
14	0.6773	-0.2594	-0.0291	0.6054	-0.3499	0.3472	0.1681	0.1209	-0.1445	-0.1817	-0.0803	0.009	0.3828	0.1286	0.0001	0.445	0.1043	-0.033	0.2674	-0.0323	0.1967	27.7728	-43.2404	31.3081
15	0.7664	-0.3453	0.1224	0.8877	-0.1387	0.6674	0.0125	0.0185	-0.0287	-0.0266	0.0036	0.0747	0.1694	0.0044	-0	0.3167	-0.0037	-0.0246	0.2033	0.0084	0.1657	23.3341	-34.4304	42.7031
16	0.6455	-0.6514	0.1813	0.649	-0.0635	0.4175	-0.0612	-0.0445	-0.0727	-0.0029	0.1162	0.1129	0.0877	-0.0831	-0	0.2724	-0.0319	-0.0222	0.2056	0.0353	0.1883	13.2866	-26.9969	40.9439

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 29:68)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 69:144)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 145:179)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 180:293)
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 29:57)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 58:92)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 93:179)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 180:293)
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESSEQ 29:57)
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESSEQ 58:144)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESSEQ 145:179)
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESSEQ 180:293)
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESSEQ 29:68)
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESSEQ 69:144)
15	X-RAY DIFFRACTION	15	CHAIN D AND (RESSEQ 145:229)
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESSEQ 230:293)

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