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

ID or keywords:

Entry

Database: PDB / ID: 3zvw

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: 2 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 28, 2011	Deposition site: PDBE / Processing site: PDBE
Supersession	Feb 29, 2012	ID: 2Y5O
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Oct 1, 2025	Group: Advisory / Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3zvw.cif.gz	735.9 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	3zvw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3zvw_validation.pdf.gz	506.1 KB	Display	wwPDB validaton report
Full document	3zvw_full_validation.pdf.gz	523.1 KB	Display
Data in XML	3zvw_validation.xml.gz	98.5 KB	Display
Data in CIF	3zvw_validation.cif.gz	140.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zv/3zvw ftp://data.pdbj.org/pub/pdb/validation_reports/zv/3zvw	HTTPS FTP

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Related structure data

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

194 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
48.2 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
48.5 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
48.5 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
48.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.748, 91.365, 107.332
Angle α, β, γ (deg.)	90.00, 94.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 7 types, 1993 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-FP5 / PHENYLACETAMIDOMETHYL BORONIC ACID Mass: 193.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₂BNO₃
#5: Chemical	ChemComp-ACN / ACETONE Mass: 58.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₆O
#6: Chemical	ChemComp-33D / 3,3-DIMETHYLBUTAN-1-OL Mass: 102.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O
#7: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1954 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.34 Å³/Da / Density % sol: 46.91 % / 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 / 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: 2→34.73 Å / Num. obs: 134070 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_merge(I) obs: 0.11 / Net I/σ(I): 11
Reflection shell	Resolution: 2→2.11 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 99

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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: 2→34.59 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.92 / SU B: 9.016 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22712	6744	5 %	RANDOM
R_work	0.17898	-	-	-
obs	0.18142	127304	99.38 %	-

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: 28.158 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.15 Å²	0 Å²	0.09 Å²
2-	-	0.24 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2→34.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	162	1954	15510

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	13762
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.22	1.973	18822
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.743	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.556	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.116	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.859	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	2173
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	10652
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	0.465	1.5	9184
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.874	2	14560
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.583	3	4578
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.543	4.5	4262
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→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	471	-
R_work	0.235	9272	-
obs	-	-	98.68 %

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	11.9689	-0.8127	8.6585	8.9375	-2.9262	6.8984	0.8427	0.4189	-1.7093	0.3254	0.4499	0.7302	0.5084	0.145	-1.2925	0.4596	-0.132	0.0165	0.2015	-0.1448	0.5798	-15.592	-28.505	37.424
2	0.8902	0.5065	0.0297	0.6145	0.1302	0.7604	-0.0532	0.1014	-0.1179	-0.0108	-0.002	0.0148	0.246	-0.2077	0.0552	0.158	-0.0467	0.0234	0.1158	-0.0291	0.0966	0.242	-15.181	34.957
3	1.3051	0.1395	-0.0085	0.4903	0.1534	0.6434	0.0193	-0.049	0.1059	0.0325	-0.0023	-0.0129	-0.0262	0.0395	-0.0169	0.1206	0.0135	-0.0033	0.08	-0.0057	0.1244	18.434	12.606	42.685
4	1.3433	-0.7384	-0.0488	0.6339	0.3351	0.4257	-0.016	-0.0215	0.0513	0.02	-0.018	0.005	-0.0066	-0.0565	0.034	0.103	0.0159	0.0044	0.0842	0.009	0.1238	-1.857	21.98	42.973
5	0.8549	0.3938	-0.0505	0.5533	0.0247	0.3244	-0.0074	0.0119	-0.0421	0.0366	-0.0028	-0.0157	0.0721	0.0028	0.0103	0.1195	0.0163	-0.002	0.0744	-0.0041	0.0965	9.802	-4.212	40.611
6	1.7583	0.1199	-0.9661	1.5014	-1.8006	5.3271	-0.1033	0.0014	-0.1445	-0.107	0.0871	0.1023	0.4536	-0.2274	0.0161	0.1256	-0.0858	0.0109	0.0845	-0.0254	0.0959	-10.091	-18.172	42.45
7	11.3979	-5.7106	10.8746	4.5731	-4.3873	11.0329	-1.1565	1.051	1.1279	-0.2621	-0.5434	0.4662	-1.5932	1.005	1.6999	0.9944	-0.1274	-0.1466	0.0978	0.0862	1.1885	54.561	47.757	14.709
8	0.3654	-0.0191	0.1216	0.3461	-0.3176	1.37	0.0046	-0.0154	0.062	0.0103	0.025	0.0184	-0.1972	-0.1373	-0.0296	0.1476	0.0203	-0.0049	0.0665	-0.0241	0.1315	55.813	26.711	39.89
9	0.2874	0.01	-0.333	0.1863	0.0554	0.6475	-0.0136	-0.082	-0.0201	0.0173	-0.0184	-0.0395	0.0424	0.0863	0.032	0.1084	0.0025	-0.0206	0.0951	0.0091	0.1051	71.465	10.248	46.92
10	0.5254	0.1367	0.2202	1.7247	-1.2561	2.811	0.0471	-0.1668	0.0175	0.1729	-0.0212	0.0537	0.0632	-0.0053	-0.0259	0.1019	-0.0157	-0.0134	0.0983	-0.0275	0.0363	62.461	12.583	65.225
11	0.423	0.2005	-0.3173	0.5051	-0.475	0.8635	0.0399	-0.0636	0.0677	0.0455	-0.0221	0.0112	-0.182	-0.0532	-0.0178	0.1337	0.0219	-0.0085	0.0566	-0.0221	0.108	56.53	29.563	37.574
12	1.6377	0.8359	0.135	3.3927	0.3784	1.0644	0.0646	-0.0303	0.2434	-0.0388	-0.0042	-0.0121	-0.2779	-0.0547	-0.0604	0.1685	0.0154	0.015	0.0227	0.0114	0.1227	61.943	39.229	24.261
13	4.7753	-0.6478	-6.5842	6.2911	0.9229	9.0955	0.6477	0.6686	0.3983	-0.4281	-0.1052	0.003	-0.8435	-0.8798	-0.5425	0.4054	0.1236	-0.1414	0.2162	0.1074	0.2002	14.053	92.571	-30.899
14	0.2968	-0.0728	0.105	0.5252	-0.4412	0.7775	-0.0184	-0.0015	0.0514	0.0054	0.0379	0.0217	-0.0451	-0.0621	-0.0195	0.1146	-0.0072	-0.0157	0.0972	-0.0196	0.1298	9.403	75.541	-12.664
15	0.8682	0.0982	-0.0635	0.3872	0.0123	0.9742	0.0142	-0.122	-0.0558	0.0472	0.0062	-0.0293	0.0677	-0.0093	-0.0205	0.1286	-0.0178	-0.0173	0.088	-0.0092	0.1142	17.123	53.632	3.678
16	1.36	-0.106	-0.869	0.0187	0.121	0.8502	-0.052	-0.061	-0.0996	0.0076	-0.0059	0.0053	0.066	0.0192	0.058	0.1242	-0.0061	-0.0106	0.0632	0.0033	0.1165	31.812	49.175	-11.064
17	0.3082	-0.009	-0.0777	0.3897	-0.3395	0.7089	-0.0018	-0.0568	0.0157	0.0151	0.0259	0.0176	0.0168	-0.0627	-0.024	0.1108	-0.0144	-0.0167	0.0897	-0.02	0.1123	9.439	65.244	-1.979
18	0.913	0.1632	0.2123	1.1088	0.0336	0.9919	-0.0391	-0.0145	0.085	0.0577	0.023	-0.0352	-0.096	0.0116	0.0161	0.1095	-0.0068	-0.0142	0.0615	-0.0156	0.1246	20.426	82.673	-17.48
19	1.1542	-0.4275	0.1574	0.5806	-0.0776	0.468	-0.0052	-0.0604	-0.1736	0.0033	-0.0015	-0.0781	0.146	0.1246	0.0067	0.1271	0.0285	0.003	0.0803	0.029	0.1287	50.557	70.63	21.704
20	2.2032	-0.6736	0.5241	0.7728	-0.2399	0.7281	0.0146	0.1003	0.0453	-0.0899	-0.0076	0.1593	-0.1005	-0.1137	-0.007	0.1274	0.0187	-0.0291	0.072	0.0153	0.1238	18.347	100.189	3.549
21	0.7609	0.4352	-0.2713	0.5626	-0.2925	0.2358	-0.0214	0.0329	0.0438	-0.0065	0.0156	-0.0183	-0.0427	0.0143	0.0059	0.119	0.0026	-0.0124	0.075	0.0067	0.1095	45.481	102.692	11.057
22	0.753	-0.1811	0.2161	0.5288	-0.1046	0.6377	-0.0283	0.0613	0.0665	-0.0248	0.0338	0.0983	-0.038	-0.1164	-0.0056	0.1088	-0.0075	-0.0129	0.075	0.0201	0.1106	28.096	96.331	7.362
23	0.6613	-0.1907	-0.0766	0.4555	0.1103	0.536	-0.022	-0.037	-0.0763	-0.017	0.0083	-0.0193	0.0437	0.0056	0.0137	0.1192	0.0006	-0.002	0.0548	0.0067	0.1122	42.32	77.257	18.008
24	1.9516	-0.2163	-0.536	1.372	0.7302	2.7511	-0.0676	0.081	-0.3268	-0.0637	-0.0308	-0.1458	0.1295	0.1204	0.0984	0.0906	0.0411	0.0206	0.0455	0.0094	0.1715	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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