PDB-2y59: Unexpected tricovalent binding mode of boronic acids within the a...

ID or keywords:

Entry

Database: PDB / ID: 2y59

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 / HYDROLASE-INHIBITOR COMPLEX / PEPTIDOGLYCAN

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: 2.5 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 12, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2017	Group: Advisory / Derived calculations Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn Item: _struct_conn.conn_type_id / _struct_conn.id ..._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.ptnr2_symmetry
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 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_symmetry
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2y59.cif.gz	677.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2y59.ent.gz	565.3 KB	Display	PDB format
PDBx/mmJSON format	2y59.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/y5/2y59 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y59	HTTPS FTP

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Related structure data

Related structure data	2y4aC 2y55C 3zvtC 3zvwC 2xdmS 1w79 1w8q 1w8y 2vgj 2vgk 2wke 2xk1 2xln S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2y4a-3 2xln-3 2y4a-2 2xdm-2 4b4z-2 2y55-1 2xln-1 2y4a-4 4ben-4 3zvt-3 1w8q-3 2xdm-4 2wke-3 3zvt-4 1w8y-4 4b4x-1 2vgj-4 4b4x-2 3zvt-1 3zvw-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 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
48.4 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
48.4 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
48.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.880, 91.353, 106.919
Angle α, β, γ (deg.)	90.00, 94.27, 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-ZA3 / TRIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO]METHYL]BORON Mass: 240.986 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀BN₂O₆
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 21 / 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.: 424 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Nonpolymer details	INHIBITOR 2-NITROBENZAMIDOMETHYLBORONIC ACID IS REPRESENTED BY TRIHYDROXY-[[(2-NITROPHENYL) ...INHIBITOR 2-NITROBENZAMIDOMETHYLBORONIC ACID IS REPRESENTED BY TRIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO] METHYL]BORON (ZA3) WITH THREE LEAVING GROUPS.

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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: 52.01 % / 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	Type: MARRESEARCH SX-165 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0724 Å / Relative weight: 1
Reflection	Resolution: 2.5→46 Å / Num. obs: 69063 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 99.8 % / R_merge(I) obs: 0.1 / Net I/σ(I): 15.1
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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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: 2.5→42 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.9 / SU B: 23.2 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.598 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25384	3493	5.1 %	RANDOM
R_work	0.19464	-	-	-
obs	0.19772	65546	99.8 %	-

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: 39.546 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.05 Å²	0 Å²	-0.1 Å²
2-	-	0.13 Å²	0 Å²
3-	-	-	-0.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	169	424	13987

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	13783
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.455	1.975	18853
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.384	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.238	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.429	15	1921
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.961	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	2170
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	10684
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	0.548	1.5	9178
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.031	2	14556
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.67	3	4605
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.695	4.5	4297
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: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.383	268	-
R_work	0.287	4797	-
obs	-	-	99.96 %

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	1.9254	0.283	2.8713	6.7629	2.4829	4.9249	0.3823	0.06	-0.1646	0.0124	-0.1732	0.235	0.6951	0.0114	-0.2091	0.6307	-0.1704	-0.0361	0.3302	-0.0264	0.3636	-15.592	-28.505	37.424
2	0.8515	0.4145	-0.2137	0.3904	0.0137	0.6727	-0.0372	0.0625	-0.1047	0.0043	0.0597	-0.0646	0.1568	-0.1763	-0.0226	0.1185	-0.0207	-0.0123	0.1784	-0.0124	0.1553	0.242	-15.181	34.957
3	1.6929	0.2216	0.3421	0.4648	0.4364	1.0264	0.0007	-0.0482	0.095	0.013	-0.0169	-0.0168	-0.0186	0.0524	0.0161	0.1034	0.0094	-0.0106	0.1171	-0.0117	0.1773	18.434	12.606	42.685
4	1.8392	-1.1109	0.0991	0.8601	0.1237	0.4551	-0.0091	-0.0413	0.0112	0.0148	-0.0433	0.0107	-0.0445	-0.0399	0.0523	0.1181	0.0071	0.0061	0.1485	-0.0213	0.1675	-1.857	21.98	42.973
5	0.7285	0.4738	0.1495	0.4744	0.1053	0.5158	-0.0306	0.0354	-0.0115	0.0442	0.0347	-0.0105	0.0831	0.0031	-0.0041	0.112	0.0136	0.0017	0.1289	-0.009	0.1693	9.802	-4.212	40.611
6	1.5175	0.19	-0.6574	0.7126	0.3492	2.707	-0.1165	0.0541	-0.1029	0.0833	0.0206	0.0338	0.4219	-0.107	0.0959	0.0998	-0.0812	0.0133	0.2011	-0.0045	0.1463	-10.091	-18.172	42.45
7	8.6033	4.552	12.5476	8.2631	10.1913	20.4573	-1.001	0.1348	0.3706	-1.2403	0.0316	0.7937	-1.9701	0.1008	0.9694	1.118	0.0215	0.0471	0.4153	0.2518	0.3316	54.561	47.757	14.709
8	0.2474	0.1168	0.1065	0.2653	-0.2169	1.2976	0.0085	-0.0676	0.0923	0.0284	0.0512	0.0425	-0.2253	-0.1458	-0.0597	0.1723	0.0786	0.0263	0.0885	-0.0166	0.1701	55.813	26.711	39.89
9	0.3277	-0.0955	-0.5724	0.2012	0.0471	1.1062	0.0099	-0.0666	-0.0104	0.0199	-0.023	-0.0027	0.0147	0.1211	0.0131	0.132	-0.0031	-0.0159	0.1287	0.0065	0.186	71.465	10.248	46.92
10	0.6477	-0.1746	0.6878	1.9063	-2.1287	4.4783	0.0605	-0.2225	0.0503	0.2702	-0.0233	0.0117	0.0272	-0.0002	-0.0373	0.1127	-0.0117	0.0044	0.1041	-0.0551	0.0948	62.461	12.583	65.225
11	0.2746	0.3356	-0.5197	0.7365	-0.7492	1.4294	0.0887	-0.0165	-0.0088	0.0735	-0.0215	0.0125	-0.3501	-0.157	-0.0672	0.1995	0.0772	0.0235	0.0948	0.0046	0.1856	56.53	29.563	37.574
12	1.8031	0.9922	-0.0357	5.2273	0.8776	2.1923	0.0099	-0.054	0.1638	-0.2759	0.1295	0.0863	-0.4697	-0.0852	-0.1394	0.2634	0.0629	0.0455	0.0331	0.0328	0.1605	61.943	39.229	24.261
13	6.9003	-3.1103	-2.6217	16.1221	3.691	8.9826	0.0357	0.6146	0.5209	-0.7308	0.2733	0.3304	-1.0871	-0.2295	-0.309	0.1951	0.025	0.0059	0.1167	0.1023	0.1996	14.053	92.571	-30.899
14	0.4025	-0.0821	0.125	0.4558	-0.1288	0.1924	-0.028	-0.0403	0.0947	0.0589	0.0486	0.0737	-0.0924	-0.1458	-0.0206	0.1711	0.025	0.0194	0.1616	-0.0152	0.1633	9.403	75.541	-12.664
15	0.7602	0.027	0.0388	0.4588	-0.0929	1.3361	0.0147	-0.0666	-0.0717	0.0796	0.0407	0.025	0.0065	-0.0092	-0.0554	0.1585	-0.0075	-0.001	0.1153	-0.0012	0.1424	17.123	53.632	3.678
16	1.5072	-0.0817	-1.3769	0.0299	0.0961	1.6972	-0.0822	-0.0747	-0.082	0.0221	0.0029	-0.0036	0.1584	0.0588	0.0793	0.1517	-0.0064	-0.0049	0.0775	0.0099	0.2124	31.812	49.175	-11.064
17	0.2655	0.0948	0.0715	0.3958	-0.3982	0.7496	-0.0063	-0.075	0.0625	0.0734	0.0163	0.0121	-0.0473	-0.1132	-0.0099	0.1405	0.018	0.0176	0.1403	-0.0251	0.1628	9.439	65.244	-1.979
18	0.9757	-0.1585	-0.0237	1.5266	-0.2238	1.5457	0.0217	-0.0387	0.0725	0.0713	0.0249	-0.0813	-0.2317	-0.0477	-0.0466	0.1627	-0.0015	0.0147	0.0615	-0.0266	0.1826	20.426	82.673	-17.48
19	1.3742	-0.4938	0.0664	0.7191	-0.0672	0.1352	-0.1088	-0.0864	-0.2991	-0.1416	-0.0074	-0.102	0.1525	-0.0047	0.1162	0.248	0.0117	0.1834	0.0746	0.065	0.3221	50.557	70.63	21.704
20	3.314	-2.1827	0.3505	2.3819	0.3988	2.9919	-0.0333	0.031	0.0625	-0.3991	0.3361	0.1668	-0.1167	-0.6109	-0.3029	0.2003	-0.2152	-0.1236	0.42	0.2295	0.1268	18.347	100.189	3.549
21	2.1808	1.3977	-0.8657	1.3828	-1.1061	1.1437	-0.067	0.1755	0.0207	-0.0222	0.0141	-0.0636	0.0244	-0.0637	0.0529	0.1243	0.0176	0.0003	0.1147	0.0072	0.148	45.481	102.692	11.057
22	1.7677	0.0683	0.0196	1.5318	-0.8829	1.1413	-0.146	0.235	0.1623	-0.2857	0.281	0.0186	0.0897	-0.3506	-0.1349	0.1575	-0.043	-0.0089	0.1727	0.0356	0.0668	28.096	96.331	7.362
23	1.7068	-0.1722	-0.5579	0.2937	0.0646	1.279	-0.2098	-0.0376	-0.2413	-0.1428	0.0051	-0.1173	0.1473	-0.0972	0.2047	0.143	-0.0198	0.099	0.0352	-0.0056	0.2531	42.32	77.257	18.008
24	2.6775	-1.1766	-0.0106	1.7958	2.8287	7.0373	-0.2072	-0.0785	-0.5921	-0.0206	-0.159	0.2368	0.0518	-0.0571	0.3662	0.1346	0.107	0.2348	0.1748	0.1494	0.4607	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
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