PDB-5ncd: Crystal structure of the polysaccharide deacetylase Bc1974 from B...

ID or keywords:

Entry

Database: PDB / ID: 5ncd

Title

Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2-amino-5-(diaminomethylideneamino)-N-hydroxypentanamide

Components

Peptidoglycan N-acetylglucosamine deacetylase

Keywords

HYDROLASE / CE4 domain / polysaccharide deacetylase / PgdA / Bacillus cereus / hydroxamate ligand

Function / homology

Function and homology information

peptidoglycan-N-acetylglucosamine deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding / membrane / plasma membrane
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.447 Å

Authors

Giastas, P. / Andreou, A. / Eliopoulos, E.E.

Citation

Journal: Biochemistry / Year: 2018
Title: Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors.
Authors: Giastas, P. / Andreou, A. / Papakyriakou, A. / Koutsioulis, D. / Balomenou, S. / Tzartos, S.J. / Bouriotis, V. / Eliopoulos, E.E.

History

Deposition	Mar 3, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ncd.cif.gz	348.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ncd.ent.gz	289.3 KB	Display	PDB format
PDBx/mmJSON format	5ncd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ncd_validation.pdf.gz	500 KB	Display	wwPDB validaton report
Full document	5ncd_full_validation.pdf.gz	512.8 KB	Display
Data in XML	5ncd_validation.xml.gz	33 KB	Display
Data in CIF	5ncd_validation.cif.gz	45.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nc/5ncd ftp://data.pdbj.org/pub/pdb/validation_reports/nc/5ncd	HTTPS FTP

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Related structure data

Related structure data	5n1jC 5n1pC 5nc6C 5nc9C 5nekC 5nelC C: citing same article (ref.)
Similar structure data	5nel-d 5n1j-d 5nc9-d 5n1p-d 4ian-d 5em2-2 3mq1-d 5nge-d 3lx9-d 1yrx-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: Peptidoglycan N-acetylglucosamine deacetylase

B: Peptidoglycan N-acetylglucosamine deacetylase

C: Peptidoglycan N-acetylglucosamine deacetylase

D: Peptidoglycan N-acetylglucosamine deacetylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	50.647, 117.438, 99.488
Angle α, β, γ (deg.)	90.00, 102.92, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Peptidoglycan N-acetylglucosamine deacetylase / Peptidoglycan-N-acetylglucosamine deacetylase / Polysaccharide deacetylase Mass: 27884.674 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) Gene: AT268_30040, B4155_0776, TQ94_03800, TU58_19865, WR51_09920, WR52_09510 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A3VTA3, UniProt: Q81EJ6*PLUS

#1: Protein

Peptidoglycan N-acetylglucosamine deacetylase / Peptidoglycan-N-acetylglucosamine deacetylase / Polysaccharide deacetylase

Mass: 27884.674 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus cereus (bacteria)
Gene: AT268_30040, B4155_0776, TQ94_03800, TU58_19865, WR51_09920, WR52_09510
Production host:

Escherichia coli (E. coli) / References: UniProt: A0A0A3VTA3, UniProt: Q81EJ6*PLUS

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Non-polymers , 5 types, 154 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: Zn
#4: Chemical	ChemComp-AHL / N-HYDROXY-L-ARGININAMIDE / L-ARGININE HYDROXAMATE Mass: 189.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₅N₅O₂
#5: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.59 Å³/Da / Density % sol: 52.43 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 100 mM Na citrate, 10% ethanol, 30% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.447→48.484 Å / Num. obs: 80836 / % possible obs: 99.48 % / Redundancy: 6.1 % / Net I/σ(I): 7.6
Reflection shell	Resolution: 2.45→2.54 Å / Num. unique obs: 4057 / % possible all: 96.28

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.447→48.484 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 35.68

	R_factor	Num. reflection	% reflection
R_free	0.2924	4044	5 %
R_work	0.226	-	-
obs	0.2294	80836	98.05 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.447→48.484 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6598	0	42	145	6785

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6849
X-RAY DIFFRACTION	f_angle_d	1.211	9247
X-RAY DIFFRACTION	f_dihedral_angle_d	14.509	2516
X-RAY DIFFRACTION	f_chiral_restr	0.042	959
X-RAY DIFFRACTION	f_plane_restr	0.006	1211

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 (%)
2.4473-2.4761	0.3622	116	0.333	2250	X-RAY DIFFRACTION	83
2.4761-2.5062	0.4089	141	0.3288	2687	X-RAY DIFFRACTION	99
2.5062-2.538	0.3869	144	0.3277	2682	X-RAY DIFFRACTION	99
2.538-2.5714	0.3585	138	0.3178	2617	X-RAY DIFFRACTION	99
2.5714-2.6066	0.3956	140	0.3496	2701	X-RAY DIFFRACTION	98
2.6066-2.6438	0.3986	136	0.3328	2647	X-RAY DIFFRACTION	99
2.6438-2.6833	0.399	145	0.328	2716	X-RAY DIFFRACTION	99
2.6833-2.7252	0.4136	138	0.315	2650	X-RAY DIFFRACTION	99
2.7252-2.7699	0.3822	140	0.3119	2688	X-RAY DIFFRACTION	99
2.7699-2.8176	0.3861	145	0.321	2711	X-RAY DIFFRACTION	99
2.8176-2.8689	0.3652	134	0.2942	2591	X-RAY DIFFRACTION	99
2.8689-2.924	0.3866	144	0.2913	2691	X-RAY DIFFRACTION	99
2.924-2.9837	0.3496	142	0.2737	2686	X-RAY DIFFRACTION	99
2.9837-3.0486	0.2939	139	0.2432	2622	X-RAY DIFFRACTION	99
3.0486-3.1195	0.3412	144	0.2414	2703	X-RAY DIFFRACTION	99
3.1195-3.1975	0.3082	140	0.2444	2670	X-RAY DIFFRACTION	99
3.1975-3.2839	0.3417	138	0.2438	2596	X-RAY DIFFRACTION	98
3.2839-3.3805	0.3128	144	0.2241	2698	X-RAY DIFFRACTION	98
3.3805-3.4896	0.2478	138	0.2073	2584	X-RAY DIFFRACTION	97
3.4896-3.6143	0.3176	140	0.2038	2676	X-RAY DIFFRACTION	99
3.6143-3.759	0.2891	142	0.202	2649	X-RAY DIFFRACTION	98
3.759-3.93	0.2878	141	0.1966	2669	X-RAY DIFFRACTION	99
3.93-4.1371	0.252	141	0.1889	2666	X-RAY DIFFRACTION	99
4.1371-4.3961	0.2602	138	0.1852	2652	X-RAY DIFFRACTION	98
4.3961-4.7353	0.2343	141	0.1712	2699	X-RAY DIFFRACTION	99
4.7353-5.2113	0.218	140	0.1713	2637	X-RAY DIFFRACTION	99
5.2113-5.9642	0.24	139	0.1903	2665	X-RAY DIFFRACTION	98
5.9642-7.5098	0.2365	136	0.2054	2623	X-RAY DIFFRACTION	97
7.5098-48.4937	0.2366	140	0.1975	2666	X-RAY DIFFRACTION	99

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	6.629	-0.9831	-0.8995	2.0602	-0.2953	2.3348	0.4203	0.0083	0.2349	0.0225	0.0944	-0.5684	0.3106	0.3502	-0.2669	0.8232	0.009	0.0358	0.569	-0.1887	0.4615	24.9795	-1.1547	91.9454
2	2.0357	0.5924	0.7446	2.1703	0.8567	2.3135	0.0761	0.2171	-0.0956	-0.5764	0.1904	-0.0026	0.8591	0.1381	-0.2024	0.9188	0.0345	-0.1147	0.367	-0.026	0.3831	12.6936	-4.3461	92.3515
3	1.9621	1.0849	0.5919	6.0958	4.4852	3.3234	0.3219	-0.2099	-0.3838	-0.0864	-0.0045	0.1304	0.8745	-0.1375	-0.1162	0.93	-0.0653	-0.1126	0.3181	0.0512	0.4606	9.2777	-7.9502	103.2549
4	1.6022	-0.2932	-0.3632	1.7695	0.4959	0.1887	0.0227	0.2804	-0.0042	-0.8693	0.0272	0.2739	0.5058	0.005	-0.0805	0.7777	-0.0301	-0.1566	0.3212	-0.0457	0.466	17.4239	3.9264	100.9184
5	2.4646	-0.0848	0.7556	2.9347	-1.1177	2.7109	-0.2312	0.2128	0.3967	-0.7114	0.214	-0.1203	-0.4733	0.5633	-0.0118	1.0072	-0.0257	0.0229	0.5778	-0.1004	0.5075	23.8784	7.401	86.5373
6	0.4146	0.1091	1.0419	1.5064	-0.0975	2.707	0.0948	0.8731	0.1947	-1.1931	-0.2227	-0.2989	-0.82	0.8369	0.1124	1.1435	-0.1692	0.1409	0.8031	-0.0696	0.4262	25.7875	2.7288	81.0111
7	2.7559	0.7899	-0.9031	2.6669	-1.0259	5.0798	-0.1998	0.2234	-0.8547	-0.0939	0.0583	-0.3717	0.976	0.6128	0.175	0.7012	0.1035	-0.1254	0.5062	-0.1431	0.5312	27.4758	-1.7594	101.4698
8	2.4345	0.7842	0.9054	3.5599	0.0004	3.2649	0.1506	0.0235	-0.4463	0.4988	0.062	-0.4069	0.9256	0.4362	-0.1603	0.7997	0.1532	-0.2095	0.3739	-0.0444	0.4483	28.802	3.8833	132.5924
9	2.2295	0.2793	0.3537	2.4843	-0.1165	1.8488	-0.0405	-0.2031	0.0591	1.1263	0.0526	0.2003	0.0435	-0.1511	-0.0465	0.9759	0.0014	-0.0758	0.3574	0.0194	0.3838	17.0773	12.9466	142.7063
10	1.2788	1.0051	-0.6243	4.1306	-0.2449	4.36	0.0953	-0.1572	0.0234	0.5346	0.0557	-0.3897	-0.2217	0.4693	-0.089	0.4231	0.0315	-0.1514	0.3254	-0.0323	0.4275	30.9557	16.4978	131.2611
11	1.5794	-0.5463	-0.0327	2.4723	0.3582	2.6621	-0.0133	-0.4843	0.2321	0.7578	0.1296	-0.5382	-0.5614	0.4536	-0.0838	1.0347	-0.0607	-0.2167	0.446	-0.0526	0.4992	33.1453	47.7676	145.9955
12	1.5509	0.0655	-0.741	1.7158	0.6658	1.7748	-0.2448	-0.2341	0.0724	0.419	0.073	-0.1521	-0.2484	-0.0393	0.1256	0.912	-0.0172	-0.0619	0.3405	-0.0279	0.3601	24.1206	41.1258	135.6194
13	1.0439	-1.0107	0.688	1.7852	-0.9647	3.1537	-0.0797	-0.1519	-0.0536	0.6478	0.3208	-0.862	0.5861	0.5522	-0.2526	0.8682	0.0809	-0.3688	0.5545	-0.1726	0.7582	40.4224	34.6165	142.8531
14	2.4882	-0.6674	-1.5072	2.9574	-1.4532	3.8593	0.2038	0.155	0.5089	0.3988	-0.1972	-0.7207	0.3298	0.7354	0.268	0.9241	0.1149	-0.364	0.8025	-0.1517	0.6966	44.3412	39.3063	147.3358
15	2.5748	0.104	1.103	3.5908	0.59	2.9424	-0.4768	0.22	0.4109	-0.6802	0.3027	-0.6161	-0.8822	0.6158	0.1365	0.7184	-0.1698	0.0205	0.4761	-0.0417	0.4947	36.2526	43.3168	128.9119
16	1.3253	-0.8316	0.8892	2.8799	0.9375	1.5453	-0.0572	-0.0476	-0.117	-0.571	0.0399	-0.2891	-0.6286	0.3736	0.1075	0.9953	-0.1692	-0.0107	0.3877	0.036	0.3829	22.505	35.5827	101.1528
17	6.0182	-1.0692	-2.6645	1.3297	1.7711	3.2355	0.3904	-0.138	0.5677	-0.641	-0.1996	-0.1108	-1.051	-0.0937	-0.2396	1.0077	-0.0642	-0.1789	0.3801	0.0586	0.5265	12.8633	43.7653	103.2057
18	3.8005	0.4062	-0.945	3.7509	-0.7313	3.1565	-0.2279	-0.0965	-0.2406	-0.6561	0.0118	0.1973	-0.3636	0.0029	0.2356	0.7546	-0.0204	-0.1078	0.3149	0.0385	0.3336	5.6706	29.8246	103.295
19	0.6984	-0.3393	-0.2304	1.8602	0.3952	0.1214	0.0082	0.2323	0.1303	-0.6691	-0.0872	0.2115	-0.0203	-0.1377	0.077	1.1373	-0.0031	-0.2331	0.3608	0.0144	0.5045	5.2772	34.8623	97.1871
20	3.186	0.6684	-1.3303	4.8495	0.112	5.3041	-0.0829	0.0401	-0.2609	-1.1056	-0.1305	0.7847	-0.1147	-0.864	-0.0458	0.7669	-0.0568	-0.185	0.3779	-0.0435	0.5981	2.3179	19.7153	97.4897
21	0.4133	0.4272	0.4056	1.2953	0.4386	1.1615	0.0624	-0.0619	0.0597	-0.2478	0.1295	0.0755	-0.0307	0.0716	0.2623	-0.0318	-0.1602	0.2617	0.5173	0.0308	0.3304	22.3569	24.5771	107.8441
22	1.9621	0.0316	-0.036	2.1098	0.748	2.8984	0.1145	0.2917	-0.0148	-0.7513	-0.045	-0.2202	-0.664	0.2413	-0.0713	0.7824	-0.0982	0.0579	0.3609	-0.0376	0.3367	25.5319	28.794	98.7601
23	2.1442	1.0134	0.8404	0.7455	1.0489	2.034	-0.0132	0.2419	-0.6054	-0.3172	-0.1029	-0.3041	-0.1781	0.008	0.0648	1.0046	-0.0529	-0.1799	0.3624	-0.0532	0.5686	10.9431	18.6918	91.9676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 68 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 140 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 141 through 156 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 157 through 204 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 205 through 233 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 234 through 250 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 251 through 273 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 68 through 119 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 120 through 183 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 184 through 273 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 68 through 118 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 119 through 204 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 205 through 233 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 234 through 249 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 250 through 273 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 68 through 102 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 103 through 118 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 119 through 140 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 141 through 166 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 167 through 183 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 184 through 219 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 220 through 261 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 262 through 273 )

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Components

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 154 molecules

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-Protein , 1 types, 4 molecules ABCD

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-Yorodumi

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Movie

-
Structure viewers

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Viewer log

-
This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

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Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 154 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi