PDB-2wke: Crystal structure of the Actinomadura R39 DD-peptidase inhibited ...

ID or keywords:

Entry

Database: PDB / ID: 2wke

Title

Crystal structure of the Actinomadura R39 DD-peptidase inhibited by 6- beta-iodopenicillanate.

Components

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

Keywords

HYDROLASE / ANTIBIOTIC RESISTANCE / ACTINOMADURA / PENICILLIN BINDING / IODOPENICILLANATE

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: 2.2 Å

Authors

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

Citation

Journal: J.Am.Chem.Soc. / Year: 2009
Title: Structural Basis of the Inhibition of Class a Beta-Lactamases and Penicillin-Binding Proteins by 6-Beta-Iodopenicillanate.
Authors: Sauvage, E. / Zervosen, A. / Dive, G. / Herman, R. / Amoroso, A. / Joris, B. / Fonze, E. / Pratt, R.F. / Luxen, A. / Charlier, P. / Kerff, F.

History

Deposition	Jun 10, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 1, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 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_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2wke.cif.gz	349.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2wke_validation.pdf.gz	497.2 KB	Display	wwPDB validaton report
Full document	2wke_full_validation.pdf.gz	525.5 KB	Display
Data in XML	2wke_validation.xml.gz	70.9 KB	Display
Data in CIF	2wke_validation.cif.gz	98.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wk/2wke ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wke	HTTPS FTP

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Related structure data

Related structure data	2wk0C 1w79S 1w8q 1w8y 2vgj 2vgk 2wix PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xk1-2 4ben-1 3zvw-4 2vgj-2 4b4z-4 2xdm-1 3zvt-3 3zvw-1 1w8y-2 1w8q-4 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

2wix
PDB Unreleased entry

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) #104 - Aug 2008 Selenocysteine Synthase 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
48.6 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
48.5 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 author&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 author&software
48.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.981, 92.686, 107.133
Angle α, β, γ (deg.)	90.00, 95.03, 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. (bacteria) / Strain: R39 References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-BIY / (3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid Mass: 217.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₁NO₄S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Co
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.21 % / Description: NONE
Crystal grow	pH: 8 / Details: pH 8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980144
Detector	Type: ADSC CCD / Detector: CCD / Date: Feb 20, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980144 Å / Relative weight: 1
Reflection	Resolution: 2.2→27 Å / Num. obs: 94213 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / R_merge(I) obs: 0.06 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.27 / Mean I/σ(I) obs: 2.9 / % possible all: 73

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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 1W79

1w79

Resolution: 2.2→29.06 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.904 / SU B: 13.453 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26136	4728	5 %	RANDOM
R_work	0.2059	-	-	-
obs	0.20862	89432	91.5 %	-

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: 21.861 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	0 Å²	0.1 Å²
2-	-	0.18 Å²	0 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	166	600	14160

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	13766
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.507	1.974	18844
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.32	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.18	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.258	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.764	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	2178
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10672
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	6442
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	9282
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	848
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	0.207	0.2	127
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.242	0.2	24
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	9354
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.825	2	14556
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.528	3	4928
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.346	4.5	4288
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→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	295	-
R_work	0.229	4888	-
obs	-	-	68.58 %

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	19.2892	-7.1188	8.4488	14.9511	7.9788	13.6928	0.5165	0.3524	-1.9187	1.1214	0.2324	0.9526	1.5178	-0.093	-0.749	0.3131	-0.1444	-0.097	0.0666	-0.0465	0.225	-16.038	-27.331	37.585
2	2.475	1.3184	-0.267	1.1029	-0.2723	0.8512	-0.0942	0.1175	-0.2798	-0.1155	0.1449	-0.1256	0.147	-0.268	-0.0507	0.1599	-0.0018	-0.0955	-0.0191	-0.0143	0.1117	1.313	-13.386	35.388
3	3.9884	0.8716	0.021	1.3048	0.4105	2.2359	0.0982	-0.2794	0.2436	0.1738	0.0486	-0.137	-0.1892	0.2161	-0.1468	0.1842	0.004	-0.0877	0.004	-0.0555	0.1049	27.874	17.143	49.056
4	1.2679	-0.2551	-0.0674	0.4878	0.3483	0.758	0.0334	0.0045	0.1146	-0.0629	-0.0387	0.0347	-0.1517	-0.0812	0.0053	0.209	0.0272	-0.1133	-0.0294	-0.0068	0.0984	8.314	15.994	41.66
5	1.7785	0.7984	-0.5525	0.4582	-0.3961	0.6681	-0.0405	0.0044	-0.1887	0.0085	0.0596	-0.1131	0.064	-0.0945	-0.0191	0.1898	0.0134	-0.1004	-0.027	-0.0115	0.1114	4.737	-9.591	38.876
6	2.344	0.1874	-0.0837	1.5734	-1.2842	5.7476	-0.1012	0.0706	-0.1712	0.0873	0.1106	0.0672	0.1179	-0.3381	-0.0094	0.1179	-0.0688	-0.1192	0.0002	0.0131	0.0973	-11.167	-16.668	41.818
7	1.0639	0.3635	-0.4204	1.0374	-0.6916	2.2369	0.0907	0.0431	0.4124	-0.1669	0.1088	0.0571	-0.5559	-0.2049	-0.1995	0.2825	0.0453	-0.0553	-0.1372	0.0033	0.2244	54.443	34.352	28.05
8	0.9385	-0.2109	1.0798	4.0622	-2.1862	5.6462	0.0546	-0.412	-0.0253	0.3464	0.0986	-0.1028	0.1672	-0.2124	-0.1532	0.1437	-0.0525	-0.0828	0.0851	-0.059	0.0547	61.133	11.033	68.837
9	0.5177	-0.0667	-0.5701	0.4705	0.1351	1.1921	-0.0286	-0.2232	0.0435	0.0483	-0.0376	-0.0481	0.1315	0.1479	0.0662	0.1742	-0.0168	-0.0978	-0.003	-0.0102	0.0783	72.023	10.077	46.726
10	0.4032	0.1534	-0.1561	1.8458	-1.8081	3.6242	0.0159	-0.2907	0.194	0.1368	-0.006	-0.0038	0.053	-0.0668	-0.0099	0.1679	-0.0643	-0.0843	-0.0086	-0.0838	0.0768	62.66	17.192	58.198
11	0.8357	0.5777	-0.4472	1.1035	-0.7519	1.4404	0.1152	-0.0787	0.134	0.0278	-0.035	-0.0659	-0.2931	-0.1304	-0.0802	0.2081	0.0053	-0.0531	-0.1234	-0.0463	0.1518	55.901	30.03	36.709
12	4.4355	1.7256	0.1562	6.9846	0.1906	1.8904	0.0371	0.0281	0.6536	-0.0318	0.1126	-0.0337	-0.5036	0.0513	-0.1496	0.3001	0.0114	-0.0292	-0.1935	0.0284	0.204	62.206	39.521	24.426
13	0.0651	-1.07	-1.5982	60.4662	-14.7694	78.4963	0.739	1.1	0.9432	2.1471	-0.02	0.3842	-5.45	-0.537	-0.719	0.3543	-0.0039	-0.0025	0.3643	0.0006	0.3549	12.238	98.189	-29.685
14	1.1838	-0.0244	-0.3174	1.7262	-1.0851	1.6254	0.026	-0.0504	0.1238	0.0612	-0.0489	0.0805	-0.1383	-0.1353	0.0229	0.2112	-0.0033	-0.1009	0.0083	-0.0728	0.1086	11.003	72.33	-9.074
15	1.5571	-0.0173	-0.327	0.8108	-0.4565	2.6917	0.0146	-0.2539	-0.0613	0.1078	-0.0398	-0.0287	0.1138	-0.0796	0.0252	0.1842	-0.022	-0.0751	0.0002	-0.028	0.0701	16.934	56.352	0.517
16	1.7271	-0.5843	-1.4871	0.2104	0.5286	1.3312	-0.0999	-0.1456	-0.156	0.072	-0.0385	-0.0109	0.1207	0.0688	0.1385	0.2147	-0.0071	-0.0861	-0.0469	0.0194	0.12	31.305	50.277	-9.768
17	0.9989	0.0389	-0.2184	0.7213	-0.4353	1.1537	0.028	-0.0891	0.1041	0.095	0.0068	0.0728	-0.0865	-0.2179	-0.0348	0.181	-0.001	-0.0953	-0.0142	-0.0797	0.0806	12.068	70.74	-5.066
18	2.6206	0.5406	0.7406	4.7813	1.0108	2.8361	-0.044	0.0612	0.1902	-0.2439	0.0773	-0.0838	-0.2983	-0.1507	-0.0332	0.2018	0.0345	-0.0771	-0.0505	-0.0057	0.0438	17.781	84.471	-21.651
19	2.444	-0.0059	0.0512	0.7227	-0.0307	0.9574	-0.0891	-0.0063	-0.6878	-0.0522	0.0016	-0.258	0.4046	0.2288	0.0875	0.2405	0.0411	-0.0124	-0.1226	0.0047	0.2979	50.671	71.793	21.342
20	1.6573	-2.3154	0.3034	4.4289	-0.5478	2.9819	0.0463	0.189	-0.0677	-0.5972	0.2431	0.6421	-0.3026	-0.5769	-0.2895	0.1713	-0.0751	-0.2148	0.1051	0.147	0.1003	19.011	101.748	3.775
21	3.2097	-0.2765	-0.2577	0.7632	-1.1321	2.7678	0.0296	-0.2454	0.1647	0.3926	0.0855	-0.0629	-0.3165	-0.0708	-0.1152	0.22	0.0062	-0.0776	-0.0563	-0.0006	0.1406	36.508	95.569	23.503
22	2.0956	0.9249	-0.1264	1.2055	-1.0501	1.2475	-0.0854	0.3379	0.1544	-0.1073	-0.0036	-0.1715	0.0288	-0.0535	0.089	0.2145	-0.0287	-0.067	-0.0794	0.0125	0.1004	46.191	105.684	8.45
23	1.3488	0.0254	-0.1348	1.7884	-0.9	1.6827	-0.1765	0.0925	-0.2085	-0.2652	0.1837	0.0503	0.1922	-0.287	-0.0073	0.2228	-0.0806	-0.0624	-0.0505	-0.0557	0.1254	32.498	85.401	15.852
24	2.5983	-0.5827	0.1458	0.2903	0.7253	3.6078	0.0818	0.3036	-0.451	-0.0387	0.0061	-0.0441	0.0854	0.2127	-0.0879	0.1637	-0.0019	0.0067	-0.0685	-0.0537	0.232	55.971	74.202	11.861

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 - 74
3	X-RAY DIFFRACTION	3	A	75 - 122
4	X-RAY DIFFRACTION	4	A	123 - 290
5	X-RAY DIFFRACTION	5	A	291 - 427
6	X-RAY DIFFRACTION	6	A	428 - 466
7	X-RAY DIFFRACTION	7	B	1 - 72
8	X-RAY DIFFRACTION	8	B	73 - 97
9	X-RAY DIFFRACTION	9	B	98 - 249
10	X-RAY DIFFRACTION	10	B	250 - 304
11	X-RAY DIFFRACTION	11	B	305 - 423
12	X-RAY DIFFRACTION	12	B	424 - 465
13	X-RAY DIFFRACTION	13	C	1 - 7
14	X-RAY DIFFRACTION	14	C	8 - 91
15	X-RAY DIFFRACTION	15	C	92 - 162
16	X-RAY DIFFRACTION	16	C	163 - 255
17	X-RAY DIFFRACTION	17	C	256 - 410
18	X-RAY DIFFRACTION	18	C	411 - 465
19	X-RAY DIFFRACTION	19	D	1 - 71
20	X-RAY DIFFRACTION	20	D	72 - 126
21	X-RAY DIFFRACTION	21	D	127 - 141
22	X-RAY DIFFRACTION	22	D	142 - 249
23	X-RAY DIFFRACTION	23	D	250 - 380
24	X-RAY DIFFRACTION	24	D	381 - 466

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