PDB-3zcz: Crystal structure of a complex between Actinomadura R39 DD-peptid...

ID or keywords:

Entry

Database: PDB / ID: 3zcz

Title

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

Components

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

Muramoylpentapeptide carboxypeptidase

Keywords

HYDROLASE /

INHIBITOR /

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 /

SIRAS / Resolution: 2.6 Å

Authors

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

Citation

Journal: Biochemistry / Year: 2013
Title: Inhibition of Dd-Peptidases by a Specific Trifluoroketone: Crystal Structure of a Complex with the Actinomadura R39 Dd-Peptidase.
Authors: Dzhekieva, L. / Adediran, S.A. / Herman, R. / Kerff, F. / Duez, C. / Charlier, P. / Sauvage, E. / Pratt, R.F.

History

Deposition	Nov 23, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
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_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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zcz.cif.gz	678.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3zcz.ent.gz	572 KB	Display	PDB format
PDBx/mmJSON format	3zcz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zc/3zcz ftp://data.pdbj.org/pub/pdb/validation_reports/zc/3zcz	HTTPS FTP

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Related structure data

Related structure data	2xdmS S: Starting model for refinement
Similar structure data	1w8y-4 2y55-2 2y55-3 1w79-1 3zvt-1 2y55-1 3zvw-1 2vgk-4 4b4x-1 2y59-4 2y4a-1 2xk1-4 2xdm-1 2y4a-3 1w79-2 2xln-2 2xk1-3 2wke-4 1w79-3 2y4a-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

2xdmS

S: Starting model for refinement

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

Unit cell

Length a, b, c (Å)	103.653, 91.727, 106.882
Angle α, β, γ (deg.)	90.00, 94.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE / Muramoylpentapeptide carboxypeptidase / DD-CARBOXYPEPTIDASE / DD-PEPTIDASE / PENICILLIN-BINDING PROTEIN / PBP Mass: 47704.055 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-516 / 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-TFR / (2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid Type: D-peptide linking / Mass: 300.275 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₉F₃N₂O₄
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 18 / 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 / Water Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.42 % / Description: NONE
Crystal grow	pH: 6.5 / Details: pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
Detector	Date: Sep 23, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 2.6→48.9 Å / Num. obs: 61653 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / R_merge(I) obs: 0.09 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

SIRAS
Starting model: PDB ENTRY 2XDM

2xdm

Resolution: 2.6→47.9 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.927 / SU B: 25.69 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 1.115 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	3120	5.1 %	RANDOM
R_work	0.193	-	-	-
obs	0.195	58482	99.94 %	-

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: 61.38 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.52 Å²	0 Å²	0.53 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→47.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13394	0	174	323	13891

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.021	13782
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.996	1.975	18868
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.2	5	1858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.868	25.47	574
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.837	15	1920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.212	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2182
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	10660
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	0.377	1.5	9194
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.709	2	14584
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.908	3	4588
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.566	4.5	4284
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: 2.6→2.667 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	247	-
R_work	0.256	4268	-
obs	-	-	99.93 %

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	43.2516	3.0295	17.5071	0.6422	1.5731	7.3719	-0.5044	-0.038	-0.765	0.0192	0.3018	0.4708	-0.1228	0.1198	0.2027	0.9131	-0.3578	-0.0549	0.2898	0.268	0.7794	-16.038	-27.331	37.585
2	0.9399	0.804	0.0601	1.2027	0.4026	0.7769	-0.0871	0.1461	-0.1525	-0.016	0.0701	-0.0624	0.1695	-0.0492	0.017	0.4348	-0.02	-0.1068	0.1432	-0.0198	0.3287	1.313	-13.386	35.388
3	5.327	2.1345	-0.152	2.6625	0.689	2.346	0.1632	-0.3786	0.3406	0.1139	-0.0198	-0.1044	-0.0894	0.1805	-0.1435	0.3541	0.0192	-0.1437	0.1398	-0.059	0.3707	27.874	17.143	49.056
4	1.4817	-0.5429	0.1277	0.6204	0.2426	0.2907	-0.0173	-0.0097	0.1377	-0.0337	0.0204	-0.0243	-0.0256	0.0027	-0.003	0.4294	0.0051	-0.1286	0.1344	-0.0007	0.353	8.314	15.994	41.66
5	1.6292	0.5903	-0.281	0.7204	-0.2406	0.9935	-0.0107	0.0313	-0.1018	0.0078	0.0543	-0.0143	0.0384	-0.0001	-0.0436	0.4266	0.0167	-0.1303	0.1271	-0.0077	0.3355	4.737	-9.591	38.876
6	1.0502	0.9375	-1.6231	2.5356	-1.245	5.8652	-0.1109	0.0968	-0.0196	-0.03	0.1858	0.1224	0.3186	-0.5849	-0.0749	0.3474	-0.0356	-0.1481	0.1544	0.0158	0.3479	-11.167	-16.668	41.818
7	0.7971	0.2412	0.0146	0.7667	-0.5892	2.4924	0.0106	0.0404	0.2148	-0.0137	0.134	0.1363	-0.3967	-0.359	-0.1446	0.4752	0.1025	-0.0743	0.0635	0.0312	0.4002	54.443	34.352	28.05
8	1.4272	-0.2818	-0.0332	3.791	-2.7197	6.4982	-0.0355	-0.2847	-0.1256	0.3281	0.1122	0.0024	0.0237	-0.3172	-0.0767	0.4159	-0.0272	-0.1207	0.2107	-0.0194	0.2643	61.133	11.033	68.837
9	0.5666	-0.212	-0.821	0.2881	0.0961	1.4945	0.0225	-0.1198	0.0149	0.027	-0.004	-0.0234	0.0959	0.1611	-0.0184	0.4217	-0.0298	-0.1375	0.1684	0.0025	0.3654	72.023	10.077	46.726
10	0.8932	0.0045	0.0585	2.4572	-2.2683	4.3303	0.0919	-0.1848	0.241	0.1685	-0.0218	-0.0001	-0.1223	0.0456	-0.0701	0.3795	-0.0331	-0.1145	0.1244	-0.089	0.2681	62.66	17.192	58.198
11	1.1542	0.6391	-0.5123	1.8578	-1.1749	2.2006	0.0834	-0.0279	0.0334	0.0619	0.0616	0.0461	-0.3648	-0.2816	-0.145	0.4341	0.0679	-0.0773	0.0486	0.0005	0.351	55.901	30.03	36.709
12	3.3004	1.733	0.576	8.3895	-0.158	2.281	-0.0552	0.1768	0.3635	-0.1082	0.1391	-0.0764	-0.4487	-0.068	-0.084	0.4863	0.0499	-0.0607	0.0223	0.0575	0.3822	62.206	39.521	24.426
13	1.0202	-5.9894	-1.9557	58.8316	-22.7248	54.7589	0.9166	0.0728	0.4488	1.571	2.5355	0.093	-5.3113	-2.9003	-3.4522	0.9927	0.4655	0.4991	0.6372	0.5379	1.274	12.238	98.189	-29.685
14	0.8148	0.1047	-0.0835	1.0269	-0.5268	0.8066	-0.0218	-0.1519	0.1424	0.0857	0.1015	0.1075	-0.1375	-0.3006	-0.0797	0.3954	0.0071	-0.1102	0.1962	-0.0647	0.2896	11.003	72.33	-9.074
15	1.1736	-0.0725	-0.2289	0.787	-0.6506	2.3456	0.0823	-0.2082	-0.0089	-0.0258	0.0416	0.0057	0.0144	-0.071	-0.1239	0.4062	-0.0626	-0.1159	0.2039	-0.0267	0.2836	16.934	56.352	0.517
16	1.7311	-0.7175	-1.6199	0.3913	0.5233	1.9669	-0.0064	-0.1653	-0.1079	-0.0102	0.0067	-0.0104	0.141	0.1294	-0.0003	0.4585	-0.0487	-0.1256	0.1515	0.0227	0.3823	31.305	50.277	-9.768
17	0.4636	0.201	-0.2527	0.7664	-0.7544	1.2465	0.0153	-0.1599	0.1016	0.093	0.0458	0.0296	-0.1223	-0.173	-0.0612	0.4128	-0.0167	-0.102	0.1948	-0.0838	0.3253	12.068	70.74	-5.066
18	2.9156	1.0283	1.0238	4.3967	1.4832	2.1779	-0.0358	0.0076	0.1932	-0.1487	0.1154	-0.0803	-0.2516	-0.2481	-0.0797	0.4328	0.0192	-0.1019	0.0737	-0.0485	0.3386	17.781	84.471	-21.651
19	1.5068	-0.2407	0.0205	0.781	-0.3492	0.5132	-0.2115	-0.0799	-0.4272	-0.1763	-0.0409	-0.284	0.3567	-0.0551	0.2523	0.5399	0.0052	0.0419	0.052	0.0412	0.5316	50.671	71.793	21.342
20	3.0132	-1.362	0.7932	3.2985	-0.3013	3.5042	-0.2009	0.2685	0.2159	-0.429	0.4258	0.3568	-0.2605	-0.565	-0.2249	0.448	-0.1013	-0.1902	0.3077	0.221	0.296	19.011	101.748	3.775
21	2.9958	0.0512	-0.2458	1.2634	-1.7208	3.7088	0.0673	-0.417	0.1268	0.2968	-0.0068	-0.161	-0.1524	-0.1491	-0.0605	0.4665	0.0307	-0.098	0.1082	-0.0262	0.3337	36.508	95.569	23.503
22	2.3123	0.6918	0.057	1.3012	-0.9248	0.8359	-0.0962	0.2632	0.1521	-0.0677	0.0188	-0.118	0.0719	0.0091	0.0774	0.4788	-0.0121	-0.0731	0.1391	0.0525	0.3458	46.191	105.684	8.45
23	1.4198	-0.0629	-0.1927	1.8481	-1.2216	1.0544	-0.2312	0.0148	-0.133	-0.212	0.2256	-0.0245	0.1717	-0.2647	0.0056	0.4715	-0.045	-0.0806	0.1024	-0.0423	0.3064	32.498	85.401	15.852
24	2.5204	-0.8981	-0.029	0.5253	-0.4306	3.6557	-0.0826	0.1365	-0.5218	-0.1723	-0.0834	-0.0663	-0.1059	0.2706	0.166	0.486	0.0126	0.1666	0.0346	-0.0581	0.616	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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