PDB-2ri1: Crystal Structure of glucosamine 6-phosphate deaminase (NagB) wit...

ID or keywords:

Entry

Database: PDB / ID: 2ri1

Title

Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P from S. mutans

Components

Glucosamine-6-phosphate deaminase

Keywords

HYDROLASE / glucosamine 6-phosphate deaminase / glucosamine 6-phosphate (GlcN6P) /

Carbohydrate metabolism

Function / homology

Function and homology information

glucosamine catabolic process / amino sugar metabolic process /

glucosamine-6-phosphate deaminase /

glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process / identical protein binding /

cytosol
Similarity search - Function

Biological species

Streptococcus mutans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 Å

Authors

Liu, C. / Li, D. / Su, X.D.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Ring-opening mechanism revealed by crystal structures of NagB and its ES intermediate complex
Authors: Liu, C. / Li, D. / Liang, Y.H. / Li, L.F. / Su, X.D.

History

Deposition	Oct 10, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ri/2ri1 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/2ri1	HTTPS FTP

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Related structure data

Related structure data	2ri0C C: citing same article (ref.)
Similar structure data	2qfo-2 5f2z-4 6yri-d 7k9r-2 4yky-d 6h34-d 2ye2-d 6cyg-2 5xrb-d 4lwi-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) 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	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: Glucosamine-6-phosphate deaminase

B: Glucosamine-6-phosphate deaminase

hetero molecules

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

1

A: Glucosamine-6-phosphate deaminase

hetero molecules

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

2

B: Glucosamine-6-phosphate deaminase

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.920, 82.480, 135.280
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Glucosamine-6-phosphate deaminase /

/ NagB / Glucosamine-6-phosphate isomerase / GNPDA / GlcN6P deaminase

Mass: 25645.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus mutans (bacteria) / Gene: SMU.636 / Plasmid: pET-28a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DV70,

glucosamine-6-phosphate deaminase

#2: Sugar

ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose

Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₄NO₈P

#3: Chemical

ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER /

Bis-tris methane

Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.93 Å³/Da / Density % sol: 58.06 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M ammonium sulfate, 0.1M bis-Tris pH 5.5, 25%(w/v) PEG 3350, vapor diffusion, hanging drop, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site: BSRF

/ Beamline: 3W1A / Wavelength: 1 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.03→19.84 Å / Num. obs: 35757 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 24.492 Å² / R_merge(I) obs: 0.079 / Net I/σ(I): 21.78

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.03-2.16		0.346	6.8	38793	5275	83.8
2.16-2.3		0.274	7.8	27051	3463	59.3
2.3-2.48		0.166	12.7	44966	5488	100
2.48-2.72		0.116	17.4	41631	5084	100
2.72-3.03		0.084	23	37807	4620	100
3.03-3.49		0.056	31.9	33527	4113	100
3.49-4.24		0.046	37.3	25204	3141	89.1
4.24-5.86		0.041	43.9	22405	2820	100
	5.86	0.038	45.1	13203	1753	96.8

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.2.0005	refinement
PDB_EXTRACT	3	data extraction
MAR345dtb		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.03→19.84 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.887 / SU B: 10.745 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.254	1773	5 %	RANDOM
R_work	0.191	-	-	-
obs	0.194	35757	90.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 5.14 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0 Å²	0 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.03→19.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3598	0	60	460	4118

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.022	3757
X-RAY DIFFRACTION	r_angle_refined_deg	2.182	1.999	5077
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.538	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	45.183	25.705	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.713	15	681
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.463	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.141	0.2	583
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2731
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1793
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	2545
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	367
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.2	0.2	47
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.245	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.541	1.5	2444
X-RAY DIFFRACTION	r_mcangle_it	0.903	2	3788
X-RAY DIFFRACTION	r_scbond_it	2.039	3	1489
X-RAY DIFFRACTION	r_scangle_it	3.266	4.5	1284

LS refinement shell

Resolution: 2.034→2.087 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.499	115	-
R_work	0.431	1767	-
all	-	1882	-
obs	-	-	65.42 %

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	13.966	4.9456	8.1321	19.1603	22.5563	26.9748	-0.3219	0.6605	1.6073	-2.0739	0.4922	0.7839	-1.4182	0.3462	-0.1703	0.1576	0.0011	-0.0399	0.0383	0.0896	0.0108	42.36	49.05	-0.499
2	0.8685	3.4274	1.4289	16.3034	0.7956	10.7925	0.4098	0.2816	-0.4053	-1.4989	0.0029	0.6853	0.2551	-0.6614	-0.4127	0.0944	0.0224	-0.0956	0.1574	-0.0149	0.0004	39.702	34.196	-6.032
3	7.6439	6.7793	2.9419	6.3765	2.1798	4.176	-0.2377	0.7415	-0.0195	-0.6193	0.264	-0.0579	-0.0901	0.2355	-0.0263	0.1274	0.0206	0.0187	0.0617	0.0123	-0.0095	54.044	39.882	-5.139
4	1.0147	0.0998	-0.2814	1.3664	0.4101	3.0815	0.0387	0.0828	-0.0414	-0.3045	0.0072	-0.0424	0.1523	0.172	-0.0459	-0.0062	0.0223	0.0191	0.0139	0.0029	0.0185	55.703	32.742	6.12
5	7.3179	2.3807	-6.6198	21.7277	-7.5411	10.0747	-0.0736	-0.5402	-0.3551	-0.5848	-0.0578	0.2272	0.5006	0.3941	0.1315	0.1014	0.0794	0.0153	0.0487	0.0152	-0.0089	55.216	21.198	17.696
6	0.6118	-1.2429	-1.5653	3.0163	2.2036	5.9431	-0.0465	-0.1478	-0.252	-0.2292	-0.0379	-0.2839	0.3573	0.4227	0.0844	-0.0107	0.0704	0.0327	0.0298	0.0241	0.0623	59.216	28.773	9.024
7	1.2853	-0.2071	1.1495	2.174	-0.3192	1.0364	-0.073	-0.3752	0.198	0.2729	0.0999	0.0132	-0.0744	0.3858	-0.0268	-0.0312	0.0257	0.0285	0.1156	-0.0191	0.0578	59.436	38.482	24.249
8	2.398	1.4066	-0.4665	2.5759	0.3273	2.396	-0.2364	0.1931	-0.0682	-0.2207	0.2175	-0.1555	-0.015	0.1655	0.0189	-0.0411	0.0189	0.0241	0.0071	0.0239	-0.0008	52.105	41.174	9.602
9	2.5043	-2.1448	-0.5229	2.2774	-0.3308	1.4858	-0.0105	-0.0806	0.0465	-0.1879	0.0075	0.1573	-0.2604	-0.061	0.003	-0.0291	0.0217	0.0468	0.008	-0.0143	0.0314	42.489	41.839	19.087
10	7.7183	6.5318	-0.691	8.9367	0.1597	0.2245	-0.0828	0.1967	0.032	0.3603	0.2822	0.2694	0.159	-0.0116	-0.1995	-0.0255	0.0106	0.0209	0.0655	0.0406	0.0078	43.198	30.469	23.428
11	7.7439	3.0874	2.9279	16.6294	3.5039	7.9163	0.1337	-0.2945	-1.3454	1.1321	0.0026	0.2494	0.8222	-0.4646	-0.1363	-0.0084	-0.0156	0.0925	0.0059	0.0751	0.2807	45.936	19.837	25.2
12	1.4862	0.4447	0.1758	4.304	-3.13	5.2619	-0.006	0.071	0.1277	0.0409	-0.0596	-0.1411	-0.333	0.0606	0.0656	-0.0528	-0.0075	0.0402	0.0012	0.0001	0.0326	50.706	44.141	13.413
13	6.2775	0.411	-4.7386	4.889	-3.4766	5.639	-0.3674	0.1738	-0.4421	-0.6524	0.3639	0.1605	0.6088	-0.3388	0.0035	0.0642	-0.0293	-0.048	0.0717	-0.0022	0.098	37.727	35.236	3.557
14	0.1416	0.6612	1.0382	3.4001	5.5626	9.2459	0.0723	0.0123	0.0792	-0.0055	-0.3388	0.4056	-0.3071	-0.735	0.2665	0.0025	0.0629	-0.0404	0.1013	0.0372	0.1132	33.996	45.433	11.062
15	0.7383	0.7863	0.0158	0.8432	-0.0213	0.2564	0.152	0.0605	0.3106	-0.4554	-0.0607	0.3125	-0.1417	0.0992	-0.0914	0.0532	0.034	0.0096	0.0316	0.028	0.0983	43.068	48.686	8.397
16	1.0524	-1.9755	-2.2137	5.1872	0.3138	14.6365	0.6784	0.4248	-0.0555	-0.6875	-0.5276	0.6232	0.2697	-1.2572	-0.1507	0.0485	0.0243	-0.1617	0.1815	0.0171	0.0352	34.356	39.202	-1.088
17	3.7479	3.1359	-1.7075	4.0045	-0.7833	3.7664	0.3924	-0.2948	0.2891	0.4303	-0.3251	0.6762	-0.1788	-0.0938	-0.0673	0.082	-0.0153	0.1361	-0.0002	-0.0633	0.046	67.022	35.675	53.93
18	9.8156	-4.9979	-0.807	6.3692	2.7669	2.9078	-0.0475	-0.7602	0.428	0.3875	-0.3809	0.0242	0.0357	-0.3657	0.4284	0.1493	0.0245	0.0457	0.0304	-0.0561	0.0457	73.832	42.27	51.736
19	3.5871	-0.3477	2.5922	3.2646	-0.4312	3.3027	-0.0354	-0.2144	0.1271	0.416	0.0268	-0.0467	-0.2444	-0.0829	0.0086	0.0068	-0.0157	0.0361	-0.0088	-0.0049	-0.0383	80.918	34.86	48.778
20	2.6953	-0.8853	1.4397	9.3761	-0.2007	1.8759	-0.0542	-0.1151	0.2377	0.3928	0.1415	-0.3237	-0.3501	0.1859	-0.0872	0.0111	-0.0192	0.0162	0.011	0.0247	-0.024	85.442	38.608	44.615
21	2.3757	0.7614	-0.1344	0.3714	0.5807	3.0628	0.0596	0.2878	0.1248	-0.0903	0.0486	-0.1975	-0.1766	0.0279	-0.1082	-0.0631	-0.0081	-0.0005	0.0104	0.0303	0.0146	80.248	29.952	29.018
22	13.7256	11.8588	0.408	16.3883	6.8971	6.9853	0.0808	0.4752	-0.2817	-0.4195	-0.0713	-0.1023	-0.4987	0.3972	-0.0095	0.0243	0.0134	0.0381	-0.0312	0.002	0.0277	84.238	38.909	35.72
23	0.7464	-0.0846	-0.9576	0.4997	1.0133	2.8987	0.0012	-0.0537	-0.2474	0.1084	0.1431	-0.5778	0.0949	0.1087	-0.1443	-0.0159	-0.0097	-0.0436	-0.0123	0.0193	0.0899	88.1	26.167	34.712
24	14.6951	1.6301	-1.1749	8.3345	6.6419	16.8194	0.0631	0.0954	-0.981	0.0123	-0.2715	-0.6041	0.5956	0.7077	0.2084	-0.0814	0.0456	0.025	-0.0198	0.0277	0.098	87.219	14.317	33.915
25	6.366	4.5119	2.8669	3.2571	2.7989	11.2205	-0.2034	-0.191	-0.3715	0.2671	-0.016	-0.3913	-0.0102	0.5363	0.2194	-0.0288	0.0709	-0.059	-0.0116	0.0277	0.1345	88.112	17.923	41.652
26	0.3464	0.452	-0.5494	2.7438	-0.7072	0.8714	-0.0099	0.0395	0.0399	0.2336	0.0379	0.1408	0.0234	0.0274	-0.028	-0.0161	0.0076	0.0258	-0.0201	-0.0296	-0.0243	73.636	25.956	43.334
27	5.1186	0.1154	-4.1686	1.5372	0.3677	4.6553	-0.1635	-0.1127	0.1502	0.1556	0.0491	-0.1927	0.1927	-0.2849	0.1144	-0.0236	-0.0406	-0.0071	-0.0599	0.0027	0.0116	71.594	14.76	40.926
28	4.8302	-1.7801	0.9647	3.9882	-3.0996	3.7489	-0.1839	0.3499	0.2297	-0.3443	0.0873	0.0898	0.1242	-0.2469	0.0965	-0.0075	-0.02	-0.035	0.0374	0.0016	0.0035	71.678	24.764	24.673
29	1.5991	0.902	-1.0909	0.537	-0.3571	3.1052	0.0034	0.0968	-0.0445	0.4331	-0.1523	-0.03	-0.1113	0.2008	0.1489	0.0443	-0.0335	-0.0225	0.0055	0.014	0.0096	76.544	23.159	48.322
30	11.5181	9.3673	-0.3086	9.0366	3.9327	12.3481	0.4692	0.1909	0.8237	-0.0695	-0.426	0.6812	-0.9769	-0.7823	-0.0431	0.0642	0.0934	0.0412	0.0147	0.0006	0.1615	61.717	34.734	43.796
31	0.3151	-0.0791	0.4452	13.8594	-0.1151	0.629	0.2264	-0.0267	0.0581	0.3966	0.0366	0.7009	0.0944	-0.2936	-0.263	0.0329	0.0029	0.1507	0.1051	-0.0139	0.1096	61.004	20.672	48.418
32	0.9248	0.2596	-0.6287	2.237	1.041	1.1123	0.301	-0.2117	0.1638	0.5723	-0.2324	0.3887	-0.0159	-0.18	-0.0686	0.084	-0.0272	0.0724	0.0407	-0.008	0.055	66.665	27.462	52.239

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-1 - 4	1 - 6
2	X-RAY DIFFRACTION	2	A	A	5 - 11	7 - 13
3	X-RAY DIFFRACTION	3	A	A	12 - 26	14 - 28
4	X-RAY DIFFRACTION	4	A	A	27 - 68	29 - 70
5	X-RAY DIFFRACTION	5	A	A	69 - 74	71 - 76
6	X-RAY DIFFRACTION	6	A	A	75 - 93	77 - 95
7	X-RAY DIFFRACTION	7	A	A	94 - 114	96 - 116
8	X-RAY DIFFRACTION	8	A	A	115 - 127	117 - 129
9	X-RAY DIFFRACTION	9	A	A	128 - 143	130 - 145
10	X-RAY DIFFRACTION	10	A	A	144 - 158	146 - 160
11	X-RAY DIFFRACTION	11	A	A	159 - 170	161 - 172
12	X-RAY DIFFRACTION	12	A	A	171 - 186	173 - 188
13	X-RAY DIFFRACTION	13	A	A	187 - 193	189 - 195
14	X-RAY DIFFRACTION	14	A	A	194 - 209	196 - 211
15	X-RAY DIFFRACTION	15	A	A	210 - 223	212 - 225
16	X-RAY DIFFRACTION	16	A	A	224 - 233	226 - 235
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22	X-RAY DIFFRACTION	22	B	B	80 - 86	82 - 88
23	X-RAY DIFFRACTION	23	B	B	87 - 102	89 - 104
24	X-RAY DIFFRACTION	24	B	B	103 - 108	105 - 110
25	X-RAY DIFFRACTION	25	B	B	109 - 115	111 - 117
26	X-RAY DIFFRACTION	26	B	B	116 - 133	118 - 135
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29	X-RAY DIFFRACTION	29	B	B	174 - 188	176 - 190
30	X-RAY DIFFRACTION	30	B	B	189 - 194	191 - 196
31	X-RAY DIFFRACTION	31	B	B	195 - 210	197 - 212
32	X-RAY DIFFRACTION	32	B	B	211 - 233	213 - 235

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