PDB-4ebn: BlaC Amoxicillin Acyl-Intermediate Complex

ID or keywords:

Entry

Database: PDB / ID: 4ebn

Title

BlaC Amoxicillin 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: 2.85 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	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2	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	4ebn.cif.gz	394.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ebn.ent.gz	326 KB	Display	PDB format
PDBx/mmJSON format	4ebn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ebn_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4ebn_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4ebn_validation.xml.gz	42.4 KB	Display
Data in CIF	4ebn_validation.cif.gz	57.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eb/4ebn ftp://data.pdbj.org/pub/pdb/validation_reports/eb/4ebn	HTTPS FTP

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Related structure data

Related structure data	4eblC 4ebpC 2gdnS 3vff 3vfh 4ebi PDB Unreleased entry 4ebm PDB Unreleased entry 4ebo PDB Unreleased entry C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ebp-3 5vpq-2 3vfh-4 6b5x-4 4rx3-d 4ebl-4 3nc8-d 4qb8-d 3zhh-3 3g30-d 5kmt-2 1hzo-1 6b5x-3 4df6-d 3bff-1 2wk0-2 3zhh-4 5zg6-1 3nck-d 5i63-2 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.)

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

Unit cell

Length a, b, c (Å)	79.567, 96.672, 109.808
Angle α, β, γ (deg.)	90.00, 107.52, 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.: 6 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-AXL / 2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID / AMOXICILLIN, bound form Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₁N₃O₅S
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: 3.57 Å³/Da / Density % sol: 65.53 %
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: 19-ID

Detector

Detector: CCD

Radiation

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

Radiation wavelength

Relative weight: 1

Reflection

Resolution: 2.85→50 Å / Num. all: 37257 / Num. obs: 37239 / % possible obs: 99.9 % / Observed criterion σ(I): 12.04 / Redundancy: 5.1 % / B_iso Wilson estimate: 60.49 Å² / Net I/σ(I): 12.04

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
2.85-2.9	5.1	2.1	1831	1	99.9
2.9-2.95	5.1	2.8	1870	1	99.9
2.95-3.01	5.1	3.2	1844	1	99.9
3.01-3.07	5.1	3.7	1853	1	99.9
3.07-3.14	5.1	4.5	1865	1	99.9
3.14-3.21	5.1	5.1	1853	1	99.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2GDN

2gdn

Resolution: 2.85→47.263 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 26.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.244	1839	4.98 %	random
R_work	0.2131	-	-	-
obs	0.2146	36951	99.25 %	-
all	-	37223	-	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 33.463 Å² / k_sol: 0.334 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.048 Å²	-0 Å²	-7.2893 Å²
2-	-	-2.3745 Å²	0 Å²
3-	-	-	0.3264 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→47.263 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7784	0	80	0	7864

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	8015
X-RAY DIFFRACTION	f_angle_d	1.662	10973
X-RAY DIFFRACTION	f_dihedral_angle_d	17.795	2813
X-RAY DIFFRACTION	f_chiral_restr	0.093	1283
X-RAY DIFFRACTION	f_plane_restr	0.012	1441

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 (%)
2.85-2.9271	0.379	139	0.3469	2640	X-RAY DIFFRACTION	97
2.9271-3.0132	0.3782	137	0.3156	2635	X-RAY DIFFRACTION	98
3.0132-3.1104	0.3015	129	0.2925	2668	X-RAY DIFFRACTION	98
3.1104-3.2216	0.3413	134	0.2735	2681	X-RAY DIFFRACTION	99
3.2216-3.3505	0.277	145	0.2533	2678	X-RAY DIFFRACTION	99
3.3505-3.503	0.2734	138	0.2229	2704	X-RAY DIFFRACTION	99
3.503-3.6876	0.225	137	0.2071	2722	X-RAY DIFFRACTION	100
3.6876-3.9185	0.2468	131	0.1997	2714	X-RAY DIFFRACTION	100
3.9185-4.2209	0.2307	136	0.1811	2731	X-RAY DIFFRACTION	100
4.2209-4.6453	0.2188	131	0.1701	2744	X-RAY DIFFRACTION	100
4.6453-5.3167	0.1932	169	0.1766	2692	X-RAY DIFFRACTION	100
5.3167-6.6955	0.2515	155	0.2293	2728	X-RAY DIFFRACTION	100
6.6955-47.2695	0.2047	158	0.1939	2775	X-RAY DIFFRACTION	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	0.4762	0.2992	-0.2938	0.3534	0.2038	0.9173	0.0893	0.5168	-0.3346	-0.4857	0.0144	0.0303	0.2004	0.0196	0.0024	0.2242	-0.0363	-0.092	0.3496	-0.0066	0.4192	27.3076	-1.4391	-5.7599
2	1.0299	0.5788	0.8972	0.7564	-0.0692	1.0531	-0.3966	-0.0052	0.677	0.3557	0.0226	-0.3841	-0.4708	0.2386	-0.0162	0.1302	-0.0227	0.0818	0.3115	-0.0461	0.1418	31.4178	17.8957	15.9672
3	0.1032	0.1297	0.0877	0.1447	0.1367	0.2194	-0.2825	0.04	0.3749	-0.2709	0.2599	0.0594	-0.2904	-0.1978	0	0.3539	-0.0505	-0.0261	0.5236	0.019	0.5257	34.8507	20.838	2.9663
4	1.083	0.7965	0.0016	1.0739	0.6682	1.4999	-0.0258	-0.0483	-0.0041	0.0195	0.0319	-0.0634	-0.0498	-0.1146	-0	0.1709	-0.0116	0.0283	0.2158	-0.0139	0.2772	29.4879	3.5915	7.4452
5	0.892	-0.1105	0.5957	1.4309	-0.2485	0.7563	0.001	-0.0246	0.1449	0.05	0.043	0.0687	-0.1571	-0.0811	0	0.3962	0.0065	0.0248	0.3705	0.0168	0.3948	6.9568	7.9516	28.0649
6	0.7101	0.07	0.4396	0.0983	-0.1015	0.7722	0.1696	-0.9403	0.0459	-0.1625	0.2935	0.1806	-0.4452	-0.8313	0.4148	0.7268	0.0861	0.1614	0.6043	-0.0595	0.7113	-3.1133	16.438	32.5286
7	0.7977	0.2168	0.6831	0.072	0.1921	0.5975	0.0965	0.9769	0.3119	0.1414	0.5578	-0.535	0.9522	0.3755	0.047	1.3369	0.0412	0.0642	1.2203	0.1713	0.6906	11.5368	19.4181	35.7513
8	0.8043	-0.2427	0.3547	0.6397	-0.9892	1.2181	0.0995	0.0587	-0.0328	0.0845	0.0918	0.1786	0.0777	0.0342	0.0196	0.3485	-0.012	0.0382	0.3118	-0.0107	0.3074	7.1983	-0.4088	33.5395
9	1.924	-0.3431	0.7813	1.5205	-0.2994	1.5161	0.1081	-0.0935	-0.1247	-0.0126	0.0439	0.0496	0.1798	-0.1971	0.0001	0.3148	-0.0247	-0.0452	0.2266	-0.0233	0.2788	12.2848	-32.5759	9.3381
10	0.6649	0.1445	-0.215	0.093	-0.1364	0.1497	0.4023	-1.2399	-0.0166	-0.3739	-0.1474	-0.0803	0.1294	0.3411	0.0316	0.7077	-0.0149	-0.0886	0.9981	0.0186	0.7088	17.2456	-41.6902	3.2723
11	1.4448	0.8402	-0.4999	0.9703	-0.2173	0.8439	-0.013	-0.0843	-0.0534	0.0723	0.051	0.0824	0.1837	0.0445	0	0.2469	0.0154	-0.0023	0.2204	-0.0047	0.1966	16.1694	-23.3949	6.125
12	0.4871	0.4593	0.1807	0.8318	-0.2161	0.6618	0.1538	-0.1086	0.2747	0.7087	-0.1446	0.0861	-0.0279	0.1894	0.0426	0.4381	0.0025	0.029	0.401	0.0496	0.4004	11.3829	-24.7916	50.6537
13	2.223	-0.4108	0.5498	0.9498	0.0415	1.24	0.0327	0.0833	-0.0362	-0.1368	0.012	-0.0204	0.1546	0.1797	0.0004	0.444	0.0289	-0.0021	0.3101	-0.01	0.2919	25.8046	-38.2373	37.8212
14	0.5754	-0.746	0.4783	0.8796	-0.2329	0.9756	0.0816	0.0781	-0.2278	-0.0928	-0.0135	0.1426	0.1324	-0.2461	-0	0.3299	0.0183	-0.0241	0.2771	0.0151	0.3589	14.0892	-26.6455	41.2907

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 29:57)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 58:144)
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 29:144)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 145:164)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 165:179)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 180:293)
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESSEQ 29:154)
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESSEQ 155:179)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESSEQ 180:293)
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESSEQ 29:68)
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESSEQ 69:229)
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESSEQ 230:293)

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