PDB-4rye: The crystal structure of D-ALANYL-D-ALANINE CARBOXYPEPTIDASE from...

ID or keywords:

Entry

Database: PDB / ID: 4rye

Title

The crystal structure of D-ALANYL-D-ALANINE CARBOXYPEPTIDASE from Mycobacterium tuberculosis H37Rv

Components

D-alanyl-D-alanine carboxypeptidase

Keywords

HYDROLASE / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Structures Of MTB Proteins Conferring Susceptibility To Known MTB Inhibitors / MTBI

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Serine-type carboxypeptidases / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / periplasmic space / proteolysis
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.901 Å

Authors

Cuff, M. / Tan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Citation

Journal: To be Published
Title: The crystal structure of D-ALANYL-D-ALANINE CARBOXYPEPTIDASE from Mycobacterium tuberculosis H37Rv
Authors: Cuff, M. / Tan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A.

History

Deposition	Dec 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 28, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4rye.cif.gz	395.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4rye_validation.pdf.gz	440.1 KB	Display	wwPDB validaton report
Full document	4rye_full_validation.pdf.gz	442.9 KB	Display
Data in XML	4rye_validation.xml.gz	48.3 KB	Display
Data in CIF	4rye_validation.cif.gz	65.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ry/4rye ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4rye	HTTPS FTP

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Related structure data

Similar structure data	4wcc-d 2ypc-d 4kxm-2 3b02-d 4p0m-d 6hdg-d 4j4h-4 2yq9-d 5udn-2 6g10-d 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
Other databases	TargetTrack: MCSG-APC105964

Similar structure data

Other databases

TargetTrack: MCSG-APC105964

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Links

PDB pages	PDBj / wwPDB / NCBI

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

111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-alanyl-D-alanine carboxypeptidase

defined by author&software
27.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: D-alanyl-D-alanine carboxypeptidase

defined by author&software
27.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: D-alanyl-D-alanine carboxypeptidase

defined by author&software
27.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: D-alanyl-D-alanine carboxypeptidase

defined by author&software
27.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.485, 88.485, 493.905
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	D-alanyl-D-alanine carboxypeptidase / Penicillin-binding protein DacB2 / Probable penicillin-binding protein DacB2 / D-alanyl-D-alanine ...Penicillin-binding protein DacB2 / Probable penicillin-binding protein DacB2 / D-alanyl-D-alanine carboxypeptidase / DD-peptidase / DD-carboxypeptidase / PBP / DD-transpeptidase / Serine-type D-ala-D-ala carboxypeptidase Mass: 27869.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: dacB2 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: I6Y204
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H₂O
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: 2.5 Å³/Da / Density % sol: 50.87 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1M Ammonium tartrate Dibasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2012 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 1.9→45 Å / Num. all: 91668 / Num. obs: 91668 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 7 % / B_iso Wilson estimate: 15.7 Å² / R_merge(I) obs: 0.085 / Net I/σ(I): 21.5
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.583 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4474 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD	Builder/HKL3000	phasing
MLPHARE	Builder/HKL3000	phasing
DM	Builder/HKL3000	model building
DENZO	Builder/HKL3000	data reduction
SCALEPACK	Builder/HKL3000	data scaling
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM	Builder/HKL3000	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.901→44.617 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 19.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2045	4338	4.87 %	random
R_work	0.1732	-	-	-
obs	0.1747	89017	97.04 %	-
all	-	89017	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.901→44.617 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7580	0	0	589	8169

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7721
X-RAY DIFFRACTION	f_angle_d	1.031	10553
X-RAY DIFFRACTION	f_dihedral_angle_d	13.586	2699
X-RAY DIFFRACTION	f_chiral_restr	0.062	1244
X-RAY DIFFRACTION	f_plane_restr	0.005	1405

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9009-1.9225	0.314	97	0.2447	1789	X-RAY DIFFRACTION	62
1.9225-1.9451	0.2815	95	0.2205	2106	X-RAY DIFFRACTION	75
1.9451-1.9688	0.2498	114	0.2155	2484	X-RAY DIFFRACTION	86
1.9688-1.9938	0.2306	108	0.2077	2647	X-RAY DIFFRACTION	94
1.9938-2.02	0.2543	157	0.2014	2838	X-RAY DIFFRACTION	98
2.02-2.0477	0.2402	142	0.1933	2817	X-RAY DIFFRACTION	100
2.0477-2.0769	0.2487	124	0.1848	2865	X-RAY DIFFRACTION	100
2.0769-2.1079	0.2458	151	0.1752	2893	X-RAY DIFFRACTION	100
2.1079-2.1408	0.2309	141	0.175	2810	X-RAY DIFFRACTION	100
2.1408-2.1759	0.2112	156	0.1815	2831	X-RAY DIFFRACTION	100
2.1759-2.2135	0.2114	164	0.1676	2893	X-RAY DIFFRACTION	100
2.2135-2.2537	0.2471	135	0.1756	2855	X-RAY DIFFRACTION	100
2.2537-2.2971	0.2194	137	0.1708	2851	X-RAY DIFFRACTION	100
2.2971-2.3439	0.2212	137	0.1628	2908	X-RAY DIFFRACTION	100
2.3439-2.3949	0.2177	148	0.172	2895	X-RAY DIFFRACTION	100
2.3949-2.4506	0.2126	160	0.1767	2834	X-RAY DIFFRACTION	100
2.4506-2.5119	0.1954	178	0.179	2861	X-RAY DIFFRACTION	100
2.5119-2.5798	0.2171	165	0.1748	2848	X-RAY DIFFRACTION	100
2.5798-2.6557	0.2336	161	0.1774	2885	X-RAY DIFFRACTION	100
2.6557-2.7414	0.1847	145	0.1826	2897	X-RAY DIFFRACTION	100
2.7414-2.8394	0.2394	160	0.1779	2910	X-RAY DIFFRACTION	100
2.8394-2.953	0.211	147	0.1804	2936	X-RAY DIFFRACTION	100
2.953-3.0874	0.207	139	0.1856	2888	X-RAY DIFFRACTION	100
3.0874-3.2501	0.2406	154	0.1804	2940	X-RAY DIFFRACTION	100
3.2501-3.4537	0.2098	148	0.1739	2938	X-RAY DIFFRACTION	100
3.4537-3.7202	0.1602	156	0.1599	2968	X-RAY DIFFRACTION	100
3.7202-4.0944	0.1696	132	0.1503	2994	X-RAY DIFFRACTION	100
4.0944-4.6863	0.1504	153	0.1384	3012	X-RAY DIFFRACTION	99
4.6863-5.9021	0.1742	160	0.1587	3058	X-RAY DIFFRACTION	99
5.9021-44.6294	0.1891	174	0.1859	3228	X-RAY DIFFRACTION	98

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	0.4902	1.1739	-0.1698	4.6241	-1.525	1.3402	0.1256	-0.0268	0.0298	0.2585	0.0047	0.6945	0.1136	-0.2403	-0.1211	0.1747	-0.0764	0.0229	0.1817	0.0015	0.1905	5.9604	53.2471	60.1651
2	2.6977	-0.829	0.8404	5.9357	-1.6971	1.282	0.1721	-0.1421	-0.1835	-0.0234	0.0023	0.4265	0.096	-0.1139	-0.155	0.1414	-0.0625	0.0025	0.1718	-0.0188	0.0884	10.8123	57.0023	52.8709
3	1.6946	1.4428	1.0042	2.9969	0.3211	1.6433	0.1306	-0.0514	0.5118	0.2079	-0.1266	0.0384	-0.312	0.1486	-0.0169	0.2431	-0.0729	0.0282	0.1534	-0.034	0.2533	28.5108	78.5286	55.1017
4	2.8429	0.7743	0.8158	0.6794	0.1381	1.5481	-0.0099	0.0145	0.2381	-0.0248	-0.0013	0.0946	-0.1643	0.0439	0.0093	0.2096	-0.0465	0.0201	0.1182	-0.0195	0.1387	21.5168	70.6164	49.7326
5	8.2061	1.2633	-2.1906	4.8884	-0.9335	6.7488	-0.2642	-0.3128	0.6932	0.4376	0.0082	-0.4688	-0.3169	0.4355	0.2728	0.424	-0.0982	-0.0539	0.3051	-0.1038	0.2809	32.804	78.4497	67.9427
6	2.1779	-0.2771	0.5556	2.7539	-1.0749	1.9824	0.0703	-0.2775	0.0913	0.1886	0.0052	0.1585	-0.1342	-0.2163	-0.0458	0.1702	-0.0556	0.0496	0.181	-0.031	0.1419	13.8465	59.9383	63.2777
7	2.0993	-1.6214	-1.992	2.4215	3.3004	4.5673	-0.3495	-0.6799	-0.0562	0.628	0.0979	0.2113	0.6155	-0.0597	0.2022	0.2446	-0.0681	-0.021	0.3845	-0.0223	0.1807	37.9053	51.9361	87.2288
8	4.5825	-2.6811	0.0306	2.831	1.2264	3.3744	-0.3321	-0.517	0.218	0.3254	0.2191	-0.1023	0.0097	0.0003	0.124	0.1991	-0.1054	-0.0779	0.2439	0.0219	0.1571	44.6069	54.8554	81.2996
9	2.4692	0.2562	-0.2574	1.2235	-0.4511	5.5728	0.0517	-0.1407	0.1189	0.0528	-0.1077	-0.0882	-0.1421	0.3191	-0.0232	0.1621	-0.0708	-0.0178	0.1808	-0.0482	0.177	49.0362	53.0474	62.9263
10	4.756	-0.1139	-0.5862	2.7408	0.8108	7.8193	0.1444	0.0804	-0.24	0.0712	-0.108	-0.2393	0.1121	0.2048	-0.0159	0.1811	-0.0278	0.0278	0.216	-0.0116	0.1792	50.9618	48.426	48.9162
11	2.7706	0.5536	-0.4112	0.7903	-0.0451	5.5421	0.0048	0.0194	-0.4129	0.2155	-0.1451	-0.0475	0.6874	0.039	0.0434	0.2683	-0.0686	-0.0029	0.1028	-0.019	0.1838	45.6329	43.2192	53.2477
12	1.7095	0.2117	0.2001	0.7785	0.0936	2.5406	-0.0023	-0.092	0.0027	0.0632	-0.0081	-0.2162	0.0405	0.231	0.0043	0.1671	-0.0663	-0.025	0.1307	0.0046	0.1804	50.6769	51.738	65.1752
13	7.8617	-1.1723	-2.8537	6.5037	0.3766	3.3891	0.3117	0.3747	-0.2214	-0.5434	-0.2219	0.0967	-0.0308	-0.1614	-0.0918	0.3165	-0.1389	-0.0039	0.1749	-0.0464	0.2176	35.886	42.8303	50.3986
14	3.4471	-0.9544	0.15	1.3704	0.382	2.1965	-0.082	-0.3643	-0.2102	0.1543	0.01	-0.0691	0.1122	-0.1282	0.06	0.1915	-0.0841	-0.0116	0.2073	0.0082	0.17	36.1035	49.0977	76.9699
15	0.5896	1.6018	0.4037	5.7454	1.5579	0.8911	0.0746	0.0326	-0.0114	0.2689	-0.0414	-0.5346	-0.0819	0.2498	-0.0353	0.1944	-0.0937	-0.0326	0.1994	0.0139	0.1799	36.3665	25.3293	60.36
16	3.6289	-1.264	-2.0195	6.3486	2.8992	1.973	0.117	0.0624	0.1287	-0.0651	-0.0171	-0.412	-0.1318	-0.0051	-0.1043	0.1912	-0.0472	-0.0461	0.1523	0.0328	0.0612	31.1844	21.4162	53.3146
17	2.6634	2.2551	-1.2013	2.767	-0.8388	1.1447	-0.0269	0.0354	-0.3482	-0.105	-0.0551	-0.1298	0.1805	-0.0541	0.0762	0.2244	-0.0535	-0.0312	0.1321	-0.0068	0.1939	16.7328	2.1886	52.7126
18	1.3165	0.5704	-0.3091	1.5602	0.5321	1.0092	0.0736	-0.1739	-0.0559	0.1919	-0.0549	-0.0441	0.1024	0.0824	-0.0258	0.1959	-0.0479	-0.0514	0.1424	0.0257	0.142	23.4947	16.0718	63.1127
19	2.7519	-1.7293	1.7301	3.85	-3.5506	3.4305	-0.4002	-0.5905	0.0782	0.7719	0.1467	-0.3301	-0.6578	0.0855	0.2525	0.3147	-0.0462	-0.0173	0.3351	0.0243	0.1712	5.1274	28.3424	88.3178
20	5.1241	-3.2371	-0.0528	2.8646	-1.2941	4.4305	-0.2772	-0.5093	-0.2282	0.3595	0.2371	0.1538	-0.0572	-0.2602	0.0325	0.16	-0.0647	0.0431	0.221	0.0365	0.1723	-1.8511	25.2547	82.6868
21	2.5774	-0.8069	0.4367	2.6271	2.3633	7.8758	0.0253	-0.1724	-0.3068	0.1065	-0.0212	0.3862	0.4116	-0.4245	-0.0086	0.1318	-0.0699	0.003	0.1607	0.0308	0.1709	-6.6877	26.0567	64.4384
22	4.8151	-1.1211	0.9884	5.2973	-0.4392	8.9723	0.078	0.2677	-0.0146	-0.0364	0.0278	0.281	-0.2026	-0.3565	-0.1564	0.1426	-0.0621	-0.029	0.1964	0.0262	0.1619	-9.1477	29.8467	50.0961
23	2.8008	0.5822	0.7837	0.9027	1.0324	6.7414	0.0054	-0.0325	0.3402	0.0549	-0.2149	-0.0344	-0.7301	-0.0559	0.1235	0.2244	-0.0526	-0.0043	0.1257	0.0023	0.158	-3.7812	35.3079	54.0252
24	3.495	3.1315	-2.562	4.0239	-2.564	5.8044	0.0117	-0.0248	-0.0075	-0.0365	0.0002	0.3304	0.0501	-0.4412	-0.0189	0.1115	-0.0062	-0.0064	0.187	0.0142	0.2095	-12.1642	28.7632	61.2602
25	1.6685	-0.3694	-1.2172	2.5556	0.1751	4.8017	-0.0197	-0.1052	-0.1651	0.0764	0.035	0.2369	-0.0726	-0.338	0.0021	0.1251	-0.0696	-0.0182	0.1857	0.0261	0.1579	-5.7032	26.6382	70.3588
26	7.1682	-3.0108	5.8443	4.399	-2.5439	8.7919	0.1137	0.2157	0.1526	-0.4755	-0.3242	-0.4651	-0.0886	0.1948	0.228	0.3233	-0.1106	0.0013	0.1929	0.0292	0.2084	5.9756	35.4976	50.8748
27	4.7615	-1.4175	-0.2666	1.1682	-0.3451	2.223	-0.0113	-0.1023	0.1947	0.0163	0.0246	-0.0326	-0.2319	0.0707	-0.007	0.1679	-0.0713	-0.0021	0.1224	-0.009	0.1436	5.8105	31.3924	73.6262
28	4.0364	-0.7071	0.0024	1.8905	-0.748	3.1777	-0.0836	-0.6516	0.1615	0.2335	0.083	-0.1394	-0.2886	0.1446	0.0454	0.2081	-0.056	0.0263	0.2922	-0.0081	0.1049	7.7198	29.8188	83.1572

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 122 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 123 through 198 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 199 through 214 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 215 through 291 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 28 through 49 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 50 through 67 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 68 through 82 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 83 through 96 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 97 through 122 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 123 through 198 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 199 through 214 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 215 through 291 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 28 through 49 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 50 through 67 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 68 through 176 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 177 through 291 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 28 through 49 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 50 through 67 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 68 through 82 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 83 through 96 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 97 through 122 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 123 through 152 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 153 through 198 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 199 through 214 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 215 through 257 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 258 through 291 )

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