PDB-2y4a: Unexpected tricovalent binding mode of boronic acids within the a...

ID or keywords:

Entry

Database: PDB / ID: 2y4a

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 / 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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 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	Jan 5, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2	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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y4a.cif.gz	667.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2y4a.ent.gz	558.3 KB	Display	PDB format
PDBx/mmJSON format	2y4a.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/y4/2y4a ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4a	HTTPS FTP

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Related structure data

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

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

Unit cell

Length a, b, c (Å)	103.308, 91.568, 106.871
Angle α, β, γ (deg.)	90.00, 94.37, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / DD-PEPTIDASE / DD-CARBOXYPEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP Mass: 47647.004 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-515 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP (bacteria) / Strain: R39 References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-BH6 / {[(2-chlorobenzoyl)amino]methyl}boronic acid Mass: 213.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₉BClNO₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 20 / 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
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.55 Å³/Da / Density % sol: 51.5 % / Description: NONE
Crystal grow	pH: 6 / Details: pH 6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.0724
Detector	Date: Jan 31, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0724 Å / Relative weight: 1
Reflection	Resolution: 2.7→46.1 Å / Num. obs: 53645 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / R_merge(I) obs: 0.11 / Net I/σ(I): 15.1
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC	5.5	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDM

2xdm

Resolution: 2.7→46.1 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.911 / SU B: 25.52 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	2734	5.1 %	RANDOM
R_work	0.187	-	-	-
obs	0.189	50895	97.35 %	-

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: 47.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.15 Å²	0 Å²	-0.23 Å²
2-	-	0.08 Å²	0 Å²
3-	-	-	-0.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→46.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	156	162	13712

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	13770
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.47	1.974	18834
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.4	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.519	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.089	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.502	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	2172
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	10676
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	0.59	1.5	9178
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.115	2	14556
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.65	3	4592
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.672	4.5	4278
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: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	181	-
R_work	0.308	3712	-
obs	-	-	96.43 %

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	4.1619	5.6478	6.0567	7.8826	8.545	9.3067	0.2733	0.5252	-0.4985	0.6575	0.5143	-0.7044	0.8464	0.3821	-0.7876	0.5484	-0.284	-0.1475	0.6165	0.2087	0.5972	-15.592	-28.505	37.424
2	0.5016	0.458	-0.2871	0.5784	0.2102	1.6109	-0.1241	0.1051	-0.1066	-0.0861	0.0819	-0.1183	0.2446	-0.1803	0.0422	0.3032	-0.0363	0.0094	0.2457	-0.0489	0.3386	0.242	-15.181	34.957
3	2.651	0.4449	0.5001	0.4687	0.3378	0.9584	-0.0143	0.0465	0.1525	-0.0106	-0.0164	-0.0271	0.0092	0.033	0.0306	0.251	0.0181	-0.0182	0.2921	-0.0315	0.3202	18.434	12.606	42.685
4	1.8535	-0.9834	0.0862	1.0987	-0.0065	0.014	-0.0691	-0.0469	0.0142	0.0322	0.0259	0.0435	0.0058	0.0265	0.0432	0.2905	0.0223	0.0111	0.3415	-0.0217	0.3151	-1.857	21.98	42.973
5	0.8725	0.4806	0.066	0.4922	0.1411	0.267	-0.0411	0.0549	0.0119	0.053	0.0601	-0.0445	0.1309	-0.01	-0.019	0.2831	-0.0019	0.017	0.3102	-0.0177	0.3151	9.802	-4.212	40.611
6	1.426	0.1194	-0.505	0.1738	0.3378	4.8382	-0.2494	0.0069	-0.1268	-0.0335	0.1132	-0.1142	0.5635	-0.507	0.1361	0.2805	-0.1467	0.026	0.3335	-0.0031	0.286	-10.091	-18.172	42.45
7	1.0591	1.0799	5.2152	7.139	5.4907	25.7097	-0.2608	-0.0513	0.0626	-2.0492	-0.1818	0.2674	-1.8872	-0.1789	0.4426	0.7991	-0.0352	0.0551	0.2973	0.1796	0.4163	54.561	47.757	14.709
8	0.2923	0.0768	0.363	0.3612	-0.2668	1.4591	-0.0175	-0.0731	0.0753	0.0239	0.1107	0.0888	-0.1856	-0.2305	-0.0932	0.2812	0.0805	0.0426	0.267	-0.0048	0.3299	55.813	26.711	39.89
9	0.4634	-0.1216	-0.581	0.0517	0.0693	1.1634	-0.0022	-0.0761	0.0268	0.0136	-0.0077	-0.0097	0.0435	0.1002	0.0099	0.2832	-0.0181	-0.0042	0.3023	0.0096	0.3566	71.465	10.248	46.92
10	0.6452	-0.5885	0.9175	1.1884	-2.2065	5.0403	0.0562	-0.1065	0.0678	0.1607	-0.0142	-0.0458	0.0242	0.0123	-0.0421	0.2796	-0.0441	0.0287	0.264	-0.0435	0.2411	62.461	12.583	65.225
11	0.5559	0.1852	-0.3283	0.8387	-1.1136	1.574	0.0519	0.0074	-0.0269	0.1298	0.0408	0.0325	-0.3011	-0.1536	-0.0926	0.3312	0.058	0.0326	0.246	-0.0124	0.3293	56.53	29.563	37.574
12	2.9214	2.2915	1.2966	7.2222	1.1465	1.5966	-0.0685	-0.0265	0.1443	-0.344	-0.0034	0.1307	-0.4096	-0.0853	0.0719	0.3922	0.0904	0.0382	0.1446	0.0446	0.3191	61.943	39.229	24.261
13	5.0023	-3.9114	-3.4337	14.4706	0.2869	9.617	0.2231	0.832	0.4479	-0.3748	-0.0277	0.0533	-0.9189	0.0195	-0.1954	0.301	0.0408	-0.0315	0.3064	0.0743	0.3422	14.053	92.571	-30.899
14	0.2289	-0.0494	0.0392	0.7529	-0.0495	0.0421	-0.0403	-0.0549	0.1236	0.0703	0.0568	0.0563	-0.0533	-0.1071	-0.0165	0.2889	0.0414	0.0381	0.3642	-0.0251	0.3208	9.403	75.541	-12.664
15	0.5911	-0.2246	-0.2381	0.7386	-0.7962	1.8801	0.0134	-0.0821	-0.0805	0.0414	0.0422	0.0409	0.0399	-0.0167	-0.0556	0.294	-0.0195	0.0086	0.3015	-0.0061	0.2983	17.123	53.632	3.678
16	2.8138	-0.5277	-1.5823	0.1063	0.3866	2.2534	-0.1098	-0.0449	-0.1146	0.0423	0.0214	0.0045	0.2578	0.1196	0.0883	0.3048	-0.0221	-0.0073	0.2242	0.0122	0.3715	31.812	49.175	-11.064
17	0.5691	-0.1406	0.1531	0.7271	-0.6643	0.8244	0.0124	-0.0696	0.0758	0.0434	-0.0077	0.0326	-0.0113	-0.0901	-0.0047	0.2902	-0.0123	0.0425	0.2896	-0.0381	0.318	9.439	65.244	-1.979
18	1.2363	-0.4826	0.1096	1.6428	-0.1902	1.0315	-0.0621	-0.0189	0.1384	0.0302	0.0501	-0.0784	-0.1712	-0.0554	0.012	0.3004	-0.0019	0.0094	0.2328	-0.0376	0.352	20.426	82.673	-17.48
19	0.3308	0.3674	-0.2796	0.9191	-0.5319	0.4189	-0.3864	-0.143	-0.323	-0.3996	-0.0006	-0.4629	0.3173	-0.0578	0.387	0.4472	0.1242	0.3037	0.3083	0.1264	0.6344	50.557	70.63	21.704
20	1.9548	-2.1957	1.0838	3.2501	-0.4025	4.1193	-0.0707	-0.2436	-0.0979	-0.4315	0.5119	0.2978	-0.1178	-0.5561	-0.4412	0.4263	-0.2032	-0.1511	0.4097	0.2652	0.3433	18.347	100.189	3.549
21	1.8837	1.4029	-0.8703	1.5945	-1.3839	1.4577	-0.1222	0.0165	-0.0146	-0.0831	-0.0521	-0.1434	0.0131	-0.0503	0.1742	0.2961	0.0016	0.0344	0.2461	0.0066	0.3364	45.481	102.692	11.057
22	1.2475	0.4819	0.2027	2.2445	-1.3496	1.1718	-0.2696	0.0455	0.206	-0.4452	0.4164	0.0731	0.2216	-0.3781	-0.1467	0.3312	-0.1148	-0.0292	0.3441	0.0699	0.2625	28.096	96.331	7.362
23	1.608	0.6437	-1.0701	1.1409	-0.416	1.4993	-0.4254	-0.1637	-0.2885	-0.3269	0.0703	-0.2641	0.2788	-0.1781	0.3551	0.3737	-0.0155	0.1888	0.1658	-0.0002	0.4089	42.32	77.257	18.008
24	2.024	0.615	-0.617	0.5227	0.3606	5.5897	-0.3641	-0.2535	-0.8643	-0.173	-0.2421	-0.4309	0.2071	-0.0798	0.6062	0.257	0.0501	0.3284	0.124	0.133	0.7885	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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