PDB-3zvt: Unexpected tricovalent binding mode of boronic acids within the a...

ID or keywords:

Entry

Database: PDB / ID: 3zvt

Title

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Components

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

Keywords

HYDROLASE / PEPTIDOGLYCAN / PENICILLIN-BINDING / TETRAVALENT BORON

Function / homology

Function and homology information

serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region
Similarity search - Function

Biological species

ACTINOMADURA SP.R39 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

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

Citation

Journal: J.Am.Chem.Soc. / Year: 2011
Title: Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein.
Authors: Zervosen, A. / Herman, R. / Kerff, F. / Herman, A. / Bouillez, A. / Prati, F. / Pratt, R.F. / Frere, J.M. / Joris, B. / Luxen, A. / Charlier, P. / Sauvage, E.

History

Deposition	Jul 27, 2011	Deposition site: PDBE / Processing site: PDBE
Supersession	Feb 29, 2012	ID: 2Y5R
Revision 1.0	Feb 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zvt.cif.gz	663.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3zvt.ent.gz	557.7 KB	Display	PDB format
PDBx/mmJSON format	3zvt.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/zv/3zvt ftp://data.pdbj.org/pub/pdb/validation_reports/zv/3zvt	HTTPS FTP

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Related structure data

Related structure data	2y4aC 2y55C 2y59C 3zvwC 2xdmS 1w79 1w8q 1w8y 2vgj 2vgk 2wke 2xk1 2xln S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2wke-3 2y59-2 2y55-2 3zcz-1 2xk1-3 3zvw-1 3zcz-2 2y4a-3 2wke-4 2y55-3 2xln-3 2xln-2 4b4z-2 2y4a-2 2xdm-2 2y59-4 2wke-2 2y55-1 2y4a-4 4b4x-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) 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

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	#29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

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

1

A: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

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

2

B: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

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

3

C: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

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

4

D: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	103.993, 92.227, 107.044
Angle α, β, γ (deg.)	90.00, 94.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / DD-CARBOXYPEPTIDASE / DD-PEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP Mass: 47647.004 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP.R39 (bacteria) References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-B07 / 2,6 DIMETHOXYBENZAMIDOBORONIC ACID Mass: 239.033 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄BNO₅
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
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: 2.72 Å³/Da / Density % sol: 54.2 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798
Detector	Type: MARRESEARCH SX-165 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 3.1→35.83 Å / Num. obs: 35205 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / R_merge(I) obs: 0.13 / Net I/σ(I): 9.7
Reflection shell	Resolution: 3.1→3.27 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDM

2xdm

Resolution: 3.1→35.83 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.88 / SU B: 48.348 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2541	1770	5 %	RANDOM
R_work	0.20284	-	-	-
obs	0.20537	33419	95.46 %	-

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: 61.989 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.9 Å²	0 Å²	0.39 Å²
2-	-	1.14 Å²	0 Å²
3-	-	-	-0.18 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→35.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	144	0	13538

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	13766
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.232	1.973	18824
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.982	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.111	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.315	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.066	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2174
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	10680
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.338	1.5	9178
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.63	2	14556
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.754	3	4588
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.274	4.5	4264
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: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.376	129	-
R_work	0.322	2372	-
obs	-	-	92.7 %

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	8.5528	-0.4085	11.8828	18.6772	1.9319	17.2789	0.1533	-0.0124	-1.0206	0.2584	0.8311	0.3134	0.3577	-0.2524	-0.9844	0.4076	-0.0158	0.1177	0.4731	-0.1628	0.535	-15.592	-28.505	37.424
2	1.4589	0.8706	-0.9094	1.5439	-0.1256	0.865	-0.1892	-0.0349	-0.1543	-0.1419	0.0148	0.1642	0.2673	-0.0083	0.1745	0.2825	0.0134	-0.011	0.1294	-0.036	0.325	0.242	-15.181	34.957
3	4.0595	0.5598	1.2987	1.5154	0.5024	1.6091	-0.0501	-0.0223	0.0799	0.0626	0.156	-0.1345	-0.1353	0.0845	-0.1058	0.2538	0.0099	-0.0301	0.1702	-0.0367	0.2177	18.434	12.606	42.685
4	1.4333	-0.1534	1.2734	1.4398	0.4826	1.403	-0.0769	-0.0393	0.1402	0.05	-0.0229	-0.0182	-0.0618	-0.0444	0.0998	0.2952	0.0104	-0.0235	0.2257	-0.012	0.2769	-1.857	21.98	42.973
5	1.1093	0.8094	-0.0384	1.1183	0.0582	0.4566	-0.0317	-0.0236	-0.0703	0.1527	0.0904	0.0078	0.1001	0.1162	-0.0587	0.2541	0.0303	-0.0315	0.1955	-0.0159	0.2915	9.802	-4.212	40.611
6	2.9676	1.8269	-3.0598	3.4376	0.0878	4.972	-0.254	0.097	-0.0193	0.2146	0.2001	0.127	0.6174	-0.1671	0.0539	0.2382	-0.0366	0.0018	0.3325	-0.0118	0.3147	-10.091	-18.172	42.45
7	0.053	-0.281	0.3321	14.5547	-11.0581	8.7867	0.7642	-0.1775	0.284	-3.0875	-2.7434	-0.5523	1.9464	2.252	1.9792	1.7871	0.1499	-0.5681	2.6196	-0.9373	1.8092	54.561	47.757	14.709
8	1.0946	-0.0623	-0.2299	0.6889	-0.8441	2.9371	0.1633	-0.027	0.2565	0.1078	0.1699	0.15	-0.4085	-0.4221	-0.3332	0.2857	0.0681	0.0095	0.0926	0.0132	0.232	55.813	26.711	39.89
9	0.3826	0.0492	-0.843	0.2612	-0.4636	2.911	-0.0339	-0.1542	-0.0265	0.0279	-0.0374	-0.0076	0.139	0.1653	0.0713	0.2726	-0.0114	-0.0505	0.2184	-0.0262	0.2556	71.465	10.248	46.92
10	1.5672	0.3949	0.3005	2.9088	-0.4938	2.8144	0.0246	-0.5383	-0.1018	0.2504	-0.127	0.0407	-0.0258	0.1535	0.1024	0.276	-0.0327	0.0315	0.2647	-0.0312	0.1319	62.461	12.583	65.225
11	0.9193	0.5249	-1.0682	1.059	-0.3906	2.3245	0.1619	0.0267	0.0681	0.066	0.0621	0.1367	-0.4669	-0.1959	-0.2239	0.3441	0.0953	0.0348	0.1512	0.0281	0.2581	56.53	29.563	37.574
12	3.1963	1.276	1.0183	7.0242	-1.3277	0.9569	-0.3452	0.0655	0.352	-0.3734	0.5262	0.2126	-0.3065	-0.1387	-0.1809	0.5902	0.0725	0.2762	0.1567	-0.0053	0.4136	61.943	39.229	24.261
13	1.7523	-0.2675	-1.6711	10.4343	3.3575	10.5867	0.6658	0.7452	0.5705	-1.0974	-0.2472	-0.5735	-1.3494	-0.7527	-0.4187	0.4653	0.3136	0.1279	0.3798	0.1476	0.4505	14.053	92.571	-30.899
14	0.8466	0.5196	-0.1099	0.8205	0.0773	0.1466	0.0695	0.0412	0.2713	0.056	-0.0091	0.1485	-0.1805	-0.1333	-0.0604	0.4135	0.1618	0.0361	0.2488	-0.0184	0.2813	9.403	75.541	-12.664
15	1.9404	0.0385	0.0243	1.2347	-0.3779	2.9096	0.0891	-0.3088	-0.057	0.1193	-0.0018	0.0624	-0.0045	-0.1503	-0.0873	0.2499	-0.0339	-0.0339	0.2612	-0.0453	0.1821	17.123	53.632	3.678
16	3.4398	-0.4845	-1.0881	0.086	0.1627	2.7803	-0.0551	-0.1389	-0.0125	0.0039	0.0218	-0.0648	0.3448	-0.0061	0.0334	0.3508	-0.0152	-0.0237	0.1323	0.024	0.2655	31.812	49.175	-11.064
17	0.9752	-0.1155	0.1084	1.2501	-1.139	2.0238	0.0324	-0.1438	0.096	0.1185	-0.019	0.0192	-0.1723	-0.2655	-0.0134	0.3164	0.0057	0.0373	0.1646	-0.0534	0.2096	9.439	65.244	-1.979
18	2.7146	-0.2194	0.9857	2.1311	0.1338	3.5811	-0.1016	-0.0374	0.3821	-0.0832	0.1832	-0.1936	-0.388	-0.1723	-0.0815	0.3474	0.0235	0.0359	0.0349	-0.0497	0.3017	20.426	82.673	-17.48
19	3.6979	-2.6789	-0.601	2.0209	0.5743	0.9276	-0.2392	0.2102	-0.4341	0.2602	-0.0774	0.2357	0.4787	-0.0695	0.3166	0.328	-0.1246	0.099	0.1765	-0.0958	0.3852	50.557	70.63	21.704
20	3.2663	-0.3253	2.2434	1.6761	0.4454	2.3801	0.2404	0.2954	-0.0309	-0.4097	-0.0114	0.2197	-0.1228	-0.438	-0.2291	0.3569	0.2084	-0.0929	0.8777	0.2157	0.3297	18.347	100.189	3.549
21	3.2314	1.3714	-2.3303	1.8076	-1.1215	1.7624	0.0017	0.4	0.043	-0.006	-0.0364	-0.0832	0.0191	-0.1786	0.0346	0.2263	0.0053	-0.0376	0.3105	0.0545	0.1767	45.481	102.692	11.057
22	2.2423	-0.7967	-0.8105	2.063	-0.3586	0.8405	0.003	0.8247	-0.1656	-0.3535	0.042	0.3881	0.0039	-0.3507	-0.0451	0.2294	0.0013	-0.1045	0.578	-0.0508	0.09	28.096	96.331	7.362
23	2.9552	-1.4913	-0.9297	1.0843	0.7612	1.013	-0.1339	0.287	-0.2856	0.1102	-0.0482	0.0571	0.2423	-0.3032	0.1821	0.2884	-0.1221	0.0407	0.2447	-0.1243	0.3331	42.32	77.257	18.008
24	0.4197	-0.9787	-0.0443	2.683	1.0635	4.7643	-0.0421	0.1746	-0.1154	0.2136	-0.1735	0.1317	0.6351	0.1445	0.2156	0.2962	-0.0293	0.0604	0.2608	-0.1616	0.3835	57.496	69.498	14.676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 11
2	X-RAY DIFFRACTION	2	A	12 - 71
3	X-RAY DIFFRACTION	3	A	72 - 166
4	X-RAY DIFFRACTION	4	A	167 - 250
5	X-RAY DIFFRACTION	5	A	251 - 423
6	X-RAY DIFFRACTION	6	A	424 - 466
7	X-RAY DIFFRACTION	7	B	1 - 6
8	X-RAY DIFFRACTION	8	B	7 - 93
9	X-RAY DIFFRACTION	9	B	94 - 249
10	X-RAY DIFFRACTION	10	B	250 - 288
11	X-RAY DIFFRACTION	11	B	289 - 423
12	X-RAY DIFFRACTION	12	B	424 - 465
13	X-RAY DIFFRACTION	13	C	1 - 14
14	X-RAY DIFFRACTION	14	C	15 - 78
15	X-RAY DIFFRACTION	15	C	79 - 163
16	X-RAY DIFFRACTION	16	C	164 - 250
17	X-RAY DIFFRACTION	17	C	251 - 373
18	X-RAY DIFFRACTION	18	C	374 - 465
19	X-RAY DIFFRACTION	19	D	1 - 71
20	X-RAY DIFFRACTION	20	D	72 - 125
21	X-RAY DIFFRACTION	21	D	126 - 231
22	X-RAY DIFFRACTION	22	D	232 - 299
23	X-RAY DIFFRACTION	23	D	300 - 419
24	X-RAY DIFFRACTION	24	D	420 - 466

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Yorodumi