PDB-2xk1: Crystal structure of a complex between Actinomadura R39 DD-peptid...

ID or keywords:

Entry

Database: PDB / ID: 2xk1

Title

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

Components

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

Keywords

HYDROLASE / 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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

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

Citation

Journal: Acs Med.Chem.Lett. / Year: 2011
Title: Structure Guided Development of Potent Reversibly Binding Penicillin Binding Protein Inhibitors
Authors: Woon, E.C.Y. / Zervosen, A. / Sauvage, E. / Simmons, K.J. / Ivec, M. / Inglis, S.R. / Fishwick, C.W.G. / Gobec, S. / Charlier, P. / Luxen, A. / Schofield, C.J.

History

Deposition	Jul 7, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 26, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 6, 2012	Group: Database references / Version format compliance
Revision 1.2	Jun 18, 2014	Group: Database references
Revision 1.3	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.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2xk1.cif.gz	676.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2xk1_validation.pdf.gz	496.8 KB	Display	wwPDB validaton report
Full document	2xk1_full_validation.pdf.gz	532 KB	Display
Data in XML	2xk1_validation.xml.gz	66 KB	Display
Data in CIF	2xk1_validation.cif.gz	89.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xk/2xk1 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xk1	HTTPS FTP

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Related structure data

Related structure data	2xlnC 2wk0S 1w79 1w8q 1w8y 2vgj 2vgk 2wke 2xdm S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ben-4 2wke-3 2y4a-4 4b4z-2 2y4a-2 2y55-1 2wke-4 3zvt-1 2y59-1 2y59-4 3zcz-1 2xdm-2 1w8y-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) #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
48.4 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)	154.898, 92.348, 143.829
Angle α, β, γ (deg.)	90.00, 92.25, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / DD-PEPTIDASE / DD-CARBOXYPEPTIDASE / 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-EWB / [(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) Mass: 300.137 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₁₉BNO₄
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.67 Å³/Da / Density % sol: 53.66 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796
Detector	Type: MARRESEARCH SX-165 / Detector: CCD / Date: Jan 25, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2.8→38.8 Å / Num. obs: 49784 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 12.7
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WK0

2wk0

Resolution: 2.8→27.53 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.902 / SU B: 34.12 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.264	2527	5.1 %	RANDOM
R_work	0.217	-	-	-
obs	0.219	47215	99.3 %	-

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: 48.76 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	-0.06 Å²
2-	-	0.19 Å²	0 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→27.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13390	0	168	166	13724

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	13782
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.164	1.974	18852
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.656	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.633	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.362	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.903	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	2178
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10688
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	6704
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	9350
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	566
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.186	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.209	0.2	62
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.057	0.2	8
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	0.259	1.5	9314
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.458	2	14548
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.567	3	4952
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.898	4.5	4304
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: 2.8→2.87 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	164	-
R_work	0.287	3449	-
obs	-	-	99.48 %

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	2.4447	1.518	0.6458	3.8406	1.6911	2.9451	-0.051	0.6702	-0.7867	-0.5075	0.1689	0.1174	0.4739	-0.2888	-0.1179	0.2009	0.047	-0.129	-0.0113	-0.2144	0.3825	-29.9172	22.1245	51.3792
2	1.6487	-0.3623	0.0616	1.2294	0.7843	1.3521	-0.0844	-0.4374	-0.0002	0.2221	0.0902	0.0334	0.0236	0.0539	-0.0058	0.2373	0.0203	0.0481	0.0611	0.0003	0.204	-15.7282	48.4402	83.2545
3	0.9527	-1.3007	0.3417	1.9689	0.0922	1.7403	-0.0234	0.0622	0.0967	-0.1068	-0.0636	0.2572	-0.2638	-0.2264	0.0871	0.2445	0.0232	0.041	-0.0232	-0.0104	0.2415	-30.7188	59.0726	70.0514
4	1.1283	-0.1996	-0.2001	1.4476	0.6329	0.8915	-0.047	-0.5306	-0.0271	0.2146	0.0868	0.0267	-0.1231	-0.0061	-0.0398	0.2594	0.0065	0.0354	0.0764	0.031	0.1946	-17.8732	46.2243	82.9675
5	2.4308	0.0691	0.3043	0.2979	0.2149	1.8086	0.0957	0.1194	-0.6107	0.049	0.0159	0.2313	0.1542	-0.0788	-0.1116	0.1909	-0.001	-0.0098	-0.1155	-0.0038	0.3532	-24.1039	30.2385	65.2097
6	4.6292	2.8589	-0.7307	3.891	-0.7124	2.347	-0.1735	0.238	-0.5	-0.2683	0.2193	0.1415	0.4843	-0.3909	-0.0458	0.1474	-0.0826	-0.0617	-0.0056	-0.1481	0.3367	-37.0309	23.6007	57.911
7	2.2033	-1.4911	-0.157	4.6055	-0.9527	1.4482	-0.0362	-0.4253	0.7767	0.4386	-0.2204	0.3799	-0.7023	-0.0915	0.2566	0.2426	0.0018	-0.0569	-0.0631	-0.1232	0.3456	-29.2378	83.5282	55.7519
8	1.5809	-0.3511	-2.0672	3.17	2.3141	4.5074	-0.0767	0.598	0.17	-0.4323	0.1926	-0.3143	0.0611	0.4905	-0.1159	0.0358	0.0014	0.0354	0.4267	0.1979	0.0103	-5.2734	61.7084	21.1871
9	3.0701	0.4871	0.3543	0.2005	0.2175	1.6964	-0.0123	0.5357	-0.0659	-0.1003	-0.0616	-0.0183	0.0232	0.0161	0.0739	0.1787	0.059	-0.0091	0.2493	0.07	0.0414	-27.621	54.5973	27.1539
10	1.1575	0.5508	-0.4011	1.0733	0.1663	1.1133	-0.0287	0.6141	-0.0531	-0.2901	-0.0259	-0.1692	-0.0321	0.3489	0.0545	0.1771	-0.0044	0.0339	0.3197	0.1424	0.0919	-8.2913	62.0669	24.4683
11	1.9738	-0.5732	0.2787	1.4913	-0.0843	1.3568	-0.1251	0.1358	0.7611	-0.0289	-0.04	-0.1446	-0.2571	0.2711	0.1651	0.1411	-0.0702	0.0036	-0.0139	0.1165	0.3124	-18.1297	76.7206	42.65
12	2.8073	-2.4385	1.1931	7.8598	-2.0254	4.9246	-0.099	0.1193	0.6529	0.162	-0.0325	0.2236	-0.6535	-0.0969	0.1315	0.161	-0.0455	-0.0319	-0.1572	0.0864	0.4089	-29.6616	83.1004	45.4361
13	3.1413	1.9387	-0.8781	6.6446	0.5303	1.3421	-0.1455	0.8488	0.985	-0.9197	0.0314	0.078	-0.8381	0.2368	0.1142	0.2421	0.0041	-0.1297	0.2076	0.262	0.0739	-52.2265	84.79	23.7665
14	1.67	-0.3949	0.0419	2.1788	0.0024	1.3487	0.049	-0.1391	0.0054	0.3747	-0.0134	0.5989	0.0857	-0.4552	-0.0356	0.0463	-0.0338	0.0907	0.145	-0.0958	0.2221	-71.7086	56.6082	48.9519
15	4.3445	-0.8168	0.6377	0.9923	0.0503	0.4604	0.0549	-0.1843	-0.1629	0.1102	-0.0744	0.1273	0.1342	-0.2042	0.0196	0.2882	-0.039	0.0269	0.094	-0.023	0.115	-50.4538	51.4317	49.2517
16	2.1976	0.0789	0.2105	1.2641	-0.3402	1.5683	0.0009	-0.4854	0.0239	0.1468	-0.1005	0.6436	0.2382	-0.4305	0.0997	0.1287	0.0282	0.1327	0.1708	-0.1412	0.2135	-72.254	60.3242	48.4384
17	3.0056	0.5295	0.759	2.7174	0.4405	2.0947	-0.1272	0.4169	0.7496	-0.0719	-0.0257	0.348	-0.1948	-0.2914	0.1529	0.1223	0.0574	-0.0398	-0.0039	0.067	0.2871	-60.4225	77.0712	34.1195
18	1.1452	3.5727	1.0696	11.2079	2.6659	8.2747	0.0327	0.5324	0.867	-0.6406	-0.1691	-0.5994	-0.7403	-0.0897	0.1364	0.1295	0.0751	-0.0581	-0.1393	0.2717	0.445	-49.7609	86.4552	32.3727
19	0.2532	-0.6025	0.9953	2.4309	-1.76	4.8721	0.1372	-0.502	-1.0305	0.2862	-0.2211	0.3199	0.7006	0.4653	0.0839	-0.0264	0.0468	-0.1052	0.5821	0.1777	0.1949	-48.155	22.6295	19.5699
20	0.9079	-0.1467	0.026	2.3477	-1.7567	3.564	0.033	0.1108	0.1791	-0.4111	0.261	0.4043	-0.1817	-0.213	-0.294	-0.0623	-0.0961	-0.0694	0.8003	0.0297	-0.0843	-64.4566	53.0583	-10.0899
21	0.935	1.2742	0.6251	3.5818	-0.0414	1.2995	0.071	0.1397	0.1074	0.08	0.0344	-0.153	-0.333	-0.0108	-0.1054	-0.0269	-0.0247	0.0248	0.6843	0.0844	-0.0668	-50.5682	63.2881	4.1692
22	0.0926	-0.1615	0.5807	0.2818	-1.013	3.6416	-0.4165	-0.2446	-0.3683	-1.3408	0.0249	-0.3989	-0.086	-1.1225	0.3917	0.6015	0.0027	-0.0324	0.5997	-0.0237	0.6015	-70.4226	63.7647	-15.7724
23	2.0679	-0.2557	-0.0458	1.4061	-0.5915	2.1156	0.0053	0.0366	-0.3939	-0.1356	0.0899	-0.0229	0.252	-0.1856	-0.0952	-0.0185	-0.0554	-0.0452	0.6976	-0.037	-0.054	-55.8714	36.0131	2.5186
24	3.2588	-0.9706	-3.2314	2.1327	-0.7017	4.7065	0.0431	-0.2976	-0.2973	-0.413	0.2772	-0.5103	0.1543	0.3814	-0.3203	-0.0087	0.0517	-0.0579	0.6308	-0.009	0.0194	-42.3507	28.3813	13.6459

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 52
2	X-RAY DIFFRACTION	2	A	53 - 142
3	X-RAY DIFFRACTION	3	A	143 - 251
4	X-RAY DIFFRACTION	4	A	252 - 310
5	X-RAY DIFFRACTION	5	A	311 - 421
6	X-RAY DIFFRACTION	6	A	422 - 466
7	X-RAY DIFFRACTION	7	B	1 - 48
8	X-RAY DIFFRACTION	8	B	49 - 126
9	X-RAY DIFFRACTION	9	B	127 - 243
10	X-RAY DIFFRACTION	10	B	244 - 317
11	X-RAY DIFFRACTION	11	B	318 - 404
12	X-RAY DIFFRACTION	12	B	405 - 465
13	X-RAY DIFFRACTION	13	C	1 - 54
14	X-RAY DIFFRACTION	14	C	55 - 149
15	X-RAY DIFFRACTION	15	C	150 - 250
16	X-RAY DIFFRACTION	16	C	251 - 318
17	X-RAY DIFFRACTION	17	C	319 - 421
18	X-RAY DIFFRACTION	18	C	422 - 465
19	X-RAY DIFFRACTION	19	D	1 - 44
20	X-RAY DIFFRACTION	20	D	45 - 137
21	X-RAY DIFFRACTION	21	D	138 - 254
22	X-RAY DIFFRACTION	22	D	255 - 276
23	X-RAY DIFFRACTION	23	D	277 - 429
24	X-RAY DIFFRACTION	24	D	430 - 466

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