PDB-2x71: Structural basis for the interaction of lactivicins with serine b...

ID or keywords:

Entry

Database: PDB / ID: 2x71

Title

Structural basis for the interaction of lactivicins with serine beta- lactamases

Components

BETA-LACTAMASE

Keywords

HYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC COMPLEX /

ANTIBIOTIC

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process /

beta-lactamase activity /

beta-lactamase / response to antibiotic
Similarity search - Function

Biological species

BACILLUS LICHENIFORMIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Sauvage, E. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.

Citation

Journal: J.Med.Chem. / Year: 2010
Title: Structural Basis for the Interaction of Lactivicins with Serine Beta-Lactamases.
Authors: Brown, T. / Charlier, P. / Herman, R. / Schofield, C.J. / Sauvage, E.

History

Deposition	Feb 22, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 14, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 2, 2011	Group: Database references
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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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PDBx/mmCIF format	2x71.cif.gz	119.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2x71.ent.gz	92.2 KB	Display	PDB format
PDBx/mmJSON format	2x71.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/2x71 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x71	HTTPS FTP

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Related structure data

Related structure data	2wk0S S: Starting model for refinement
Similar structure data	5zg6-2 7doo-2 3sh8-1 5ghx-2 3soi-1 3le9-2 5ghz-1 3m2k-1 5zfl-2 5k09-23 5ghy-2 3m2j-2 5ghx-1 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

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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) #13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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)
#13 - Jan 2001
Alcohol Dehydrogenase
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#44 - Aug 2003
Calmodulin
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: BETA-LACTAMASE

B: BETA-LACTAMASE

hetero molecules

59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BETA-LACTAMASE

hetero molecules

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

2

B: BETA-LACTAMASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.652, 104.089, 62.838
Angle α, β, γ (deg.)	90.00, 94.45, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	BETA-LACTAMASE / Mass: 29513.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACILLUS LICHENIFORMIS (bacteria) / Strain: BS3 / References: UniProt: P94458, beta-lactamase
#2: Chemical	ChemComp-L4C / (2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID / LACTIVICIN / Lactivicin Mass: 290.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₂O₈ / Comment: antibiotic*YM
#3: Chemical	ChemComp-EOH / ETHANOL / Ethanol Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.58 Å³/Da / Density % sol: 52.27 % / Description: NONE
Crystal grow	pH: 4 / Details: pH 4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979746
Detector	Date: Oct 15, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979746 Å / Relative weight: 1
Reflection	Resolution: 2.1→34.7 Å / Num. obs: 34702 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / R_merge(I) obs: 0.11 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WK0

2wk0

Resolution: 2.1→34.69 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.926 / SU B: 9.073 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22698	1744	5 %	RANDOM
R_work	0.18671	-	-	-
obs	0.18876	32944	99.33 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 19.225 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	-0.01 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→34.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3988	0	36	304	4328

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	4079
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.239	1.985	5514
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.17	5	508
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.787	25.161	186
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.949	15	738
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.216	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	637
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3036
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	2162
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	2840
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.128	0.2	337
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.234	0.2	48
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.25	0.2	12
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.496	1.5	2611
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.856	2	4106
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.512	3	1630
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.457	4.5	1408
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.259	134	-
R_work	0.232	2414	-
obs	-	-	99.11 %

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	1.2412	-0.7329	-0.793	1.0272	0.4797	0.9919	-0.068	-0.1426	0.1252	0.1887	0.0417	-0.138	-0.0297	0.235	0.0263	0.0983	-0.0114	-0.0054	0.1177	-0.0246	0.14	31.71	6.032	30.534
2	1.6231	0.2735	0.2643	1.0717	0.4127	0.8719	0.0303	0.124	-0.1417	-0.2382	-0.0394	0.1244	-0.0089	-0.0954	0.0091	0.116	0.0085	-0.0076	0.0434	0.0023	0.1006	10.658	-2.232	12.081
3	2.7578	0.398	0.3613	2.5455	-0.1074	2.0903	0.0108	0.2427	-0.1742	-0.111	0.0109	0.1037	0.1341	-0.0372	-0.0217	0.1108	-0.0078	0.0164	0.0527	-0.0193	0.1011	11.381	-8.632	10.079
4	2.1697	0.7368	1.0234	1.4779	1.2139	3.9226	-0.0074	-0.0176	0.2172	-0.0814	-0.0217	0.0964	-0.2905	-0.2299	0.029	0.11	0.0273	0.0043	0.0453	0.0283	0.1389	12.871	10.022	14.185
5	2.2126	0.524	0.1325	1.1964	-0.1794	2.0387	-0.0854	0.1273	0.0876	-0.0929	0.033	-0.1253	0.0092	0.103	0.0524	0.1034	0.0152	0.0104	0.0314	-0.022	0.1283	21.049	7.95	18.48
6	7.0346	-4.3595	-1.9977	3.8507	1.3545	2.6796	-0.1684	-0.5154	-0.1348	0.1769	0.2298	0.2004	0.011	-0.0843	-0.0614	0.0855	-0.0183	0.0091	0.0661	-0.0138	0.0924	8.64	-4.169	26.468
7	2.9726	-0.962	0.4517	2.3388	0.0463	7.2012	0.0335	-0.3214	-0.1922	0.307	0.0483	0.0324	0.3037	0.0689	-0.0818	0.109	0.0017	0.0033	0.0585	0.0018	0.1131	23.822	-8.058	28.044
8	2.7809	0.3604	-1.3754	1.5053	-0.2783	3.2594	0.0594	-0.1186	-0.0184	0.1192	0.0145	-0.0876	0.0494	0.1921	-0.0738	0.0784	0.0158	-0.0123	0.0577	-0.0122	0.1215	28.854	-1.004	25.749
9	0.941	-0.2007	0.6662	0.9576	0.2817	1.7515	-0.0768	0.007	-0.0148	-0.0941	-0.0076	-0.1392	-0.0252	0.0978	0.0844	0.1149	-0.0018	0.0223	0.048	0.0092	0.1287	20.171	19.403	47.34
10	7.3929	-3.3542	-5.4977	6.7358	6.183	16.3503	0.115	-0.1602	-0.4111	-0.2285	0.2114	0.6769	-0.0588	-1.7192	-0.3263	0.0615	-0.2146	0.0494	0.4691	0.1767	0.3088	-8.336	9.277	54.89
11	9.7688	1.7351	4.7693	6.8316	2.2559	10.5721	-0.1571	-0.9693	0.4672	0.5577	0.2512	0.673	-0.493	-1.554	-0.0941	0.0347	0.173	0.13	0.3812	0.0808	0.1399	-4.468	21.455	65.258
12	1.887	-0.2189	-0.4276	3.0679	0.0977	3.6733	-0.1766	-0.18	-0.227	0.2148	0.3246	0.2117	0.3242	-0.6597	-0.148	0.0601	-0.0817	0.0242	0.1805	0.0396	0.1437	3.613	12.148	57.635
13	1.6757	-0.045	-0.0454	1.0927	-0.6375	2.9473	-0.0335	-0.1528	-0.0977	0.0365	0.0027	-0.0705	0.0624	-0.0864	0.0307	0.1177	-0.0078	0.0318	0.0318	-0.003	0.1221	15.401	12.266	56.04
14	16.5826	-2.6863	-0.8639	7.366	5.3312	8.6615	-0.0969	1.1971	-0.8482	-1.3532	0.4663	0.2015	0.8333	-1.0459	-0.3694	0.2347	-0.1715	-0.0404	0.2997	-0.046	0.2272	0.459	8.969	41.336
15	1.9125	0.5104	0.5654	1.6732	0.1629	2.2281	-0.0435	0.1351	0.0411	-0.1588	0.0436	0.1577	-0.155	-0.2784	-0	0.1115	0.0188	-0.0017	0.0642	0.0045	0.1235	9.681	23.984	45.18
16	2.7814	0.5072	0.8202	2.7465	-0.1631	4.6549	-0.0014	0.0194	0.1662	0.1176	-0.0051	-0.1098	-0.1759	0.0144	0.0065	0.1304	-0.0182	-0.0013	0.0209	0.0146	0.1571	21.403	28.868	50.62

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 64
2	X-RAY DIFFRACTION	2	A	65 - 106
3	X-RAY DIFFRACTION	3	A	107 - 140
4	X-RAY DIFFRACTION	4	A	141 - 167
5	X-RAY DIFFRACTION	5	A	168 - 195
6	X-RAY DIFFRACTION	6	A	196 - 215
7	X-RAY DIFFRACTION	7	A	216 - 237
8	X-RAY DIFFRACTION	8	A	238 - 290
9	X-RAY DIFFRACTION	9	B	31 - 81
10	X-RAY DIFFRACTION	10	B	82 - 96
11	X-RAY DIFFRACTION	11	B	97 - 120
12	X-RAY DIFFRACTION	12	B	121 - 155
13	X-RAY DIFFRACTION	13	B	156 - 195
14	X-RAY DIFFRACTION	14	B	196 - 205
15	X-RAY DIFFRACTION	15	B	206 - 265
16	X-RAY DIFFRACTION	16	B	266 - 290

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