PDB-5bu9: Crystal structure of Beta-N-acetylhexosaminidase from Beutenbergi...

ID or keywords:

Entry

Database: PDB / ID: 5bu9

Title

Crystal structure of Beta-N-acetylhexosaminidase from Beutenbergia cavernae DSM 12333

Components

Beta-N-acetylhexosaminidase

Keywords

HYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Beta-N-acetylhexosaminidase

Function / homology

Function and homology information

beta-N-acetylhexosaminidase / peptidoglycan turnover / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Beutenbergia cavernae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.255 Å

Authors

Chang, C. / Tan, K. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Crystal structure of Beta-N-acetylhexosaminidase from Beutenbergia cavernae DSM 12333
Authors: Chang, C. / Tan, K. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Jun 3, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5bu9.cif.gz	265.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5bu9.ent.gz	214.9 KB	Display	PDB format
PDBx/mmJSON format	5bu9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bu/5bu9 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/5bu9	HTTPS FTP

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Related structure data

Similar structure data	1un1-2 3up8-1 4ee7-1 5afd-d 5goz-2 4bh6-2 1un1-1 5gp1-3 5z46-2 6muj-2 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-APC100057

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-N-acetylhexosaminidase

B: Beta-N-acetylhexosaminidase

hetero molecules

69.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-N-acetylhexosaminidase

hetero molecules

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

2

B: Beta-N-acetylhexosaminidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	146.510, 146.510, 85.487
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Beta-N-acetylhexosaminidase Mass: 34571.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Beutenbergia cavernae (strain ATCC BAA-8 / DSM 12333 / NBRC 16432) (bacteria) Strain: ATCC BAA-8 / DSM 12333 / NBRC 16432 / Gene: Bcav_3777 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / References: UniProt: C5C3W0, beta-N-acetylhexosaminidase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.88 Å³/Da / Density % sol: 68.3 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Bis-Tris Propane, 2.2 MDL-malic acid pH 7.0

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97921 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2013

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97921 Å / Relative weight: 1

Reflection

Resolution: 2.25→50 Å / Num. all: 54042 / Num. obs: 50001 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / B_iso Wilson estimate: 30.85 Å² / R_merge(I) obs: 0.106 / R_pim(I) all: 0.036 / R_rim(I) all: 0.113 / Χ²: 0.894 / Net I/av σ(I): 21.461 / Net I/σ(I): 7.3 / Num. measured all: 478592

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.25-2.29	9.7	0.814	2459	0.877	0.275	0.86	0.582	100
2.29-2.33	9.8	0.71	2445	0.905	0.239	0.75	0.607	100
2.33-2.38	9.8	0.634	2492	0.921	0.213	0.669	0.624	100
2.38-2.42	9.9	0.54	2457	0.935	0.181	0.57	0.67	100
2.42-2.48	9.9	0.48	2488	0.952	0.16	0.506	0.713	100
2.48-2.53	9.9	0.422	2473	0.957	0.141	0.445	0.767	100
2.53-2.6	9.9	0.372	2490	0.964	0.125	0.392	0.793	100
2.6-2.67	9.9	0.329	2483	0.965	0.11	0.347	0.843	100
2.67-2.75	9.9	0.272	2496	0.98	0.091	0.287	0.9	100
2.75-2.83	9.9	0.248	2486	0.98	0.083	0.262	0.963	100
2.83-2.94	9.8	0.203	2496	0.986	0.068	0.214	1.032	100
2.94-3.05	9.7	0.176	2496	0.987	0.06	0.186	1.086	100
3.05-3.19	9.5	0.143	2486	0.99	0.049	0.151	1.157	100
3.19-3.36	9.4	0.12	2485	0.993	0.041	0.127	1.231	100
3.36-3.57	9.1	0.096	2518	0.994	0.034	0.102	1.196	100
3.57-3.85	8.8	0.082	2517	0.995	0.03	0.088	1.155	100
3.85-4.23	8.6	0.071	2520	0.995	0.026	0.076	1.075	100
4.23-4.85	8.7	0.064	2521	0.996	0.023	0.069	0.957	100
4.85-6.1	9.5	0.06	2558	0.995	0.02	0.064	0.802	100
6.1-50	9.8	0.061	2635	0.997	0.021	0.065	0.835	99.6

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Processing

Software

Name	Version	Classification
PHENIX	(dev-2056_1692: ???)	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
HKL-3000		phasing
SBC-Collect		data collection
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.255→41.825 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.88 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1977	4671	4.88 %	Random selection
R_work	0.1584	91034	-	-
obs	0.1603	49544	98.92 %	-

Solvent computation

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

Displacement parameters

B_iso max: 112.45 Å² / B_iso mean: 36.6429 Å² / B_iso min: 17.18 Å²

Refinement step

Cycle: final / Resolution: 2.255→41.825 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4800	0	36	415	5251
B_iso mean	-	-	54.66	40.64	-
Num. residues	-	-	-	-	676

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	4935
X-RAY DIFFRACTION	f_angle_d	1.346	6761
X-RAY DIFFRACTION	f_chiral_restr	0.068	824
X-RAY DIFFRACTION	f_plane_restr	0.007	912
X-RAY DIFFRACTION	f_dihedral_angle_d	13.402	2923

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2549-2.2805	0.3344	135	0.2461	2914	3049	95
2.2805-2.3073	0.2709	157	0.228	3001	3158	98
2.3073-2.3355	0.2567	155	0.2127	3042	3197	99
2.3355-2.365	0.2441	168	0.2155	3031	3199	99
2.365-2.3961	0.2485	192	0.2	2969	3161	99
2.3961-2.429	0.2066	116	0.2006	3024	3140	98
2.429-2.4636	0.2716	148	0.1972	3108	3256	99
2.4636-2.5004	0.2028	160	0.1923	2985	3145	98
2.5004-2.5395	0.228	143	0.194	3005	3148	99
2.5395-2.5811	0.2659	180	0.1925	2998	3178	98
2.5811-2.6256	0.2317	185	0.1936	3023	3208	99
2.6256-2.6733	0.2598	146	0.1956	3028	3174	99
2.6733-2.7248	0.2604	160	0.1938	3040	3200	99
2.7248-2.7804	0.2099	156	0.2029	3072	3228	99
2.7804-2.8408	0.2723	112	0.2017	3063	3175	99
2.8408-2.9069	0.2476	185	0.1954	2983	3168	99
2.9069-2.9796	0.2595	184	0.2048	3025	3209	99
2.9796-3.0601	0.2124	144	0.1926	3036	3180	99
3.0601-3.1501	0.2225	176	0.2003	3010	3186	99
3.1501-3.2517	0.1987	146	0.1781	3082	3228	99
3.2517-3.3679	0.1933	170	0.1736	2985	3155	99
3.3679-3.5027	0.2089	136	0.1569	3069	3205	99
3.5027-3.662	0.2214	172	0.1425	3027	3199	99
3.662-3.855	0.1561	152	0.1344	3092	3244	100
3.855-4.0963	0.1601	184	0.1189	3028	3212	100
4.0963-4.4123	0.1572	130	0.1084	3089	3219	100
4.4123-4.8557	0.1368	150	0.1033	3084	3234	100
4.8557-5.5569	0.1435	116	0.1133	3087	3203	100
5.5569-6.9958	0.1532	161	0.1291	3072	3233	100
6.9958-41.8321	0.1242	152	0.1269	3062	3214	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	5.53	0.811	-1.1745	4.4857	-0.8896	1.2578	0.0688	-0.493	-0.1169	0.3045	-0.0093	-0.2263	0.1978	0.1684	-0.1173	0.3803	-0.0614	-0.0673	0.4138	-0.004	0.2499	-25.002	69.6439	40.2286
2	4.7673	0.332	-1.4139	2.4593	0.3818	1.3731	0.1885	-0.4595	-0.3521	0.3959	-0.1642	-0.0363	0.2053	-0.0102	0.0382	0.4653	-0.1508	-0.0111	0.4545	0.0167	0.2461	-32.4414	70.2617	45.9482
3	0.1352	-0.4464	0.1148	1.4992	-0.5137	2.5038	0.1867	-0.4536	0.1421	0.3134	-0.0551	0.3049	0.067	-0.5797	-0.1053	0.3852	-0.1177	0.0779	0.5195	-0.0495	0.2668	-44.6189	78.036	41.2947
4	1.482	0.1586	0.0761	0.7847	0.0876	2.2887	0.1333	-0.4386	0.3696	0.2597	-0.1102	0.2194	-0.2065	-0.4051	-0.0695	0.4262	-0.0048	0.1328	0.4384	-0.1086	0.3662	-45.892	88.3116	40.2234
5	0.5977	0.1984	-0.4794	1.1226	-0.1588	0.4214	0.1164	-0.2859	0.3564	0.2877	-0.0467	0.1926	-0.5355	-0.4644	-0.0292	0.4738	0.0354	0.1232	0.4521	-0.0988	0.4021	-44.3006	91.6809	35.5167
6	1.4929	0.2601	-0.2061	1.302	-0.3269	2.0094	0.1209	-0.0833	0.322	0.1677	-0.0201	0.0622	-0.4821	-0.196	-0.0894	0.3582	-0.0117	0.0786	0.2811	-0.0309	0.3207	-34.6319	90.4593	26.651
7	3.8695	0.425	1.0251	4.7831	4.5792	4.5484	-0.0522	-0.0287	0.5848	-0.3928	0.1094	-0.3662	-0.8112	0.4808	-0.1264	0.3789	-0.1058	0.0243	0.2896	-0.0002	0.3137	-24.1311	91.9791	27.9153
8	1.3667	-0.9824	0.2942	0.9579	-0.7727	2.0164	0.1521	-0.0785	0.0194	0.124	-0.0317	-0.035	0.0274	-0.0919	-0.1388	0.2717	-0.0925	0.0167	0.3325	-0.0299	0.2871	-27.2933	77.0588	27.7633
9	4.6775	-0.2009	-2.2845	2.9789	0.2802	2.1324	0.1241	-0.2591	0.1841	0.1589	-0.0516	-0.2678	-0.0732	0.3033	-0.0899	0.2787	-0.0506	-0.0716	0.3365	0.0052	0.3166	-16.0533	78.2649	35.2309
10	1.8037	0.2159	-0.1983	4.6828	-1.2713	0.5659	0.0356	-0.0037	-0.1552	-0.2839	0.0325	-0.3283	0.0514	0.2412	-0.1692	0.2218	0.0342	-0.0154	0.3424	-0.0488	0.3169	-42.9324	43.8385	23.8273
11	1.1665	-0.3124	-0.1313	4.0035	0.1559	1.0093	-0.0309	0.2324	-0.0628	-0.1166	0.1711	-0.3767	-0.0842	0.4426	-0.1084	0.2168	-0.0358	0.018	0.3911	-0.0408	0.2914	-41.2837	52.9581	21.7338
12	0.8166	0.3904	-0.2331	0.6109	-0.1533	1.1774	0.0454	0.0303	0.1736	0.0478	0.0182	0.0296	-0.258	0.0976	-0.0606	0.2775	-0.05	0.0224	0.2856	0.0117	0.2855	-56.3894	65.7168	29.0468
13	0.7081	0.3379	0.2007	1.0821	-0.8626	3.6092	-0.0246	-0.0602	0.0978	0.1148	-0.0244	0.134	-0.2024	-0.0257	0.0409	0.2197	-0.0126	0.0333	0.2246	0.0012	0.2705	-63.4728	63.7847	31.8865
14	0.7441	0.0592	0.0553	1.7214	-1.0528	3.9382	-0.0168	-0.0868	0.0019	0.1875	0.0227	0.1438	0.001	-0.2117	-0.0325	0.2057	-0.0239	0.0187	0.2172	-0.0213	0.2609	-65.316	51.3392	36.17
15	4.1576	-3.6278	3.2817	4.7121	-1.5668	5.3108	0.191	-0.1559	-0.3793	0.1491	-0.0787	0.4659	0.4392	-0.3397	-0.0895	0.2524	-0.0433	0.0388	0.2782	-0.0235	0.2838	-67.2714	42.5452	30.6905
16	2.0154	-1.0589	-0.7473	2.0069	0.0355	1.2023	-0.0316	0.031	0.0632	0.2196	-0.0027	-0.2133	0.0714	0.3121	0.0073	0.2301	-0.0063	-0.0433	0.2387	-0.003	0.2215	-53.0644	42.8009	34.3842
17	2.2169	1.0511	1.0298	6.4796	-1.4398	2.0102	0.1564	0.0608	-0.216	-0.2228	0.0045	-0.0813	0.5686	0.0441	-0.1174	0.2122	0.0358	0.017	0.2422	-0.0522	0.2345	-53.1406	35.2602	23.5682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 71 through 103 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 104 through 142 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 143 through 161 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 162 through 213 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 214 through 245 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 310 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 311 through 329 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 330 through 373 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 374 through 408 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 70 through 103 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 104 through 142 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 143 through 213 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 214 through 245 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 246 through 310 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 311 through 329 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 330 through 373 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 374 through 407 )	B

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Yorodumi