PDB-9npn: Crystal structure of the inactive conformation of a glycoside hyd...

ID or keywords:

Entry

Database: PDB / ID: 9npn

Title

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E465A Mutant) from the GH2 family in the space group P1 at 3.1 A

Components

Glycoside hydrolase family 2

Keywords

HYDROLASE / Redox-regulation / glycosyl hydrolase / mannosidase / redox-switch / metagenome / disulfide bond

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Martins, M.P. / Spadeto, J.P.M. / Miyamoto, R.Y. / Morais, M.A.B. / Murakami, M.T.

Funding support

Brazil, 3items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2021/04891-3	Brazil
Sao Paulo Research Foundation (FAPESP)	2021/09793-0	Brazil
Sao Paulo Research Foundation (FAPESP)	2022/06298-0	Brazil

Citation

Journal: To Be Published
Title: Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E465A Mutant) from the GH2 family in the space group P1 at 3.1 A
Authors: Martins, M.P. / Spadeto, J.P.M. / Miyamoto, R.Y. / Morais, M.A.B. / Murakami, M.T.

History

Deposition	Mar 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9npn.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb9npn.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	9npn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9npn_validation.pdf.gz	526.2 KB	Display	wwPDB validaton report
Full document	9npn_full_validation.pdf.gz	573.5 KB	Display
Data in XML	9npn_validation.xml.gz	166.1 KB	Display
Data in CIF	9npn_validation.cif.gz	209 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9npn ftp://data.pdbj.org/pub/pdb/validation_reports/np/9npn	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycoside hydrolase family 2

B: Glycoside hydrolase family 2

C: Glycoside hydrolase family 2

D: Glycoside hydrolase family 2

E: Glycoside hydrolase family 2

F: Glycoside hydrolase family 2

hetero molecules

547 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycoside hydrolase family 2

B: Glycoside hydrolase family 2

C: Glycoside hydrolase family 2

hetero molecules

defined by author&software
Evidence: gel filtration, electron microscopy
274 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Glycoside hydrolase family 2

F: Glycoside hydrolase family 2

hetero molecules

D: Glycoside hydrolase family 2

hetero molecules

defined by author&software
274 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.278, 123.715, 133.041
Angle α, β, γ (deg.)	89.13, 117.56, 103.51
Int Tables number	1
Space group name H-M	P1

#1: Protein	Glycoside hydrolase family 2 Mass: 90758.555 Da / Num. of mol.: 6 / Mutation: E465A Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: beta-mannosidase
#2: Chemical	... ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.19 Å³/Da / Density % sol: 61.48 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.75 M ammonium phosphate dibasic, 0.1 M imidazole, pH 8, 0.2 M sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 1.36999 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2020

Radiation

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

Radiation wavelength

Wavelength: 1.36999 Å / Relative weight: 1

Reflection

Resolution: 3.1→49.15 Å / Num. obs: 119969 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC_1/2: 0.982 / R_merge(I) obs: 0.126 / R_rim(I) all: 0.178 / Net I/σ(I): 3.45

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
3.1-3.29	0.678	6682	0.662	0.958	1
3.29-3.51	0.515	6570	0.583	0.728	1
3.51-3.79	0.29	5935	0.879	0.41	1
3.79-4.15	0.206	5280	0.899	0.291	1
4.15-4.64	0.143	4501	0.957	0.203	1
4.64-5.35	0.112	3737	0.972	0.158	1
5.35-6.53	0.109	3177	0.975	0.155	1
6.53-9.16	0.068	2447	0.989	0.096	1
9.16-49.15	0.035	1226	0.997	0.049	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→49.15 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2763	5993	5 %
R_work	0.245	-	-
obs	0.2466	119815	98.05 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.1→49.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34670	0	150	189	35009

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	35674
X-RAY DIFFRACTION	f_angle_d	0.663	48402
X-RAY DIFFRACTION	f_dihedral_angle_d	11.65	12975
X-RAY DIFFRACTION	f_chiral_restr	0.052	5094
X-RAY DIFFRACTION	f_plane_restr	0.012	6268

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 (%)
3.1-3.14	0.4124	194	0.3701	3688	X-RAY DIFFRACTION	97
3.14-3.17	0.4113	203	0.3694	3846	X-RAY DIFFRACTION	97
3.17-3.21	0.3901	194	0.3482	3675	X-RAY DIFFRACTION	97
3.21-3.25	0.3837	201	0.3357	3826	X-RAY DIFFRACTION	97
3.25-3.29	0.3391	195	0.319	3707	X-RAY DIFFRACTION	98
3.29-3.34	0.3298	203	0.3002	3840	X-RAY DIFFRACTION	98
3.34-3.39	0.3207	197	0.2871	3748	X-RAY DIFFRACTION	98
3.39-3.44	0.3283	198	0.2798	3774	X-RAY DIFFRACTION	98
3.44-3.49	0.2981	199	0.2766	3782	X-RAY DIFFRACTION	98
3.49-3.55	0.305	201	0.2741	3820	X-RAY DIFFRACTION	98
3.55-3.61	0.2611	198	0.2645	3775	X-RAY DIFFRACTION	98
3.61-3.68	0.2984	196	0.2601	3761	X-RAY DIFFRACTION	98
3.68-3.75	0.2795	202	0.2576	3837	X-RAY DIFFRACTION	98
3.75-3.82	0.2813	199	0.2481	3777	X-RAY DIFFRACTION	98
3.82-3.91	0.2913	201	0.2353	3804	X-RAY DIFFRACTION	98
3.91-4	0.2778	200	0.2346	3794	X-RAY DIFFRACTION	98
4-4.1	0.2518	199	0.2335	3785	X-RAY DIFFRACTION	98
4.1-4.21	0.2845	200	0.2341	3796	X-RAY DIFFRACTION	98
4.21-4.33	0.3002	199	0.2273	3781	X-RAY DIFFRACTION	98
4.33-4.47	0.2561	202	0.2162	3823	X-RAY DIFFRACTION	98
4.47-4.63	0.2299	201	0.2107	3813	X-RAY DIFFRACTION	98
4.63-4.81	0.2419	196	0.2133	3750	X-RAY DIFFRACTION	98
4.81-5.03	0.2293	200	0.2105	3792	X-RAY DIFFRACTION	98
5.03-5.3	0.2469	202	0.2199	3835	X-RAY DIFFRACTION	98
5.3-5.63	0.2612	202	0.2278	3830	X-RAY DIFFRACTION	99
5.63-6.06	0.2539	203	0.2376	3852	X-RAY DIFFRACTION	99
6.06-6.67	0.2647	200	0.2438	3807	X-RAY DIFFRACTION	99
6.67-7.64	0.2869	202	0.2282	3833	X-RAY DIFFRACTION	99
7.64-9.61	0.2141	204	0.214	3866	X-RAY DIFFRACTION	100
9.61-49.15	0.2638	202	0.229	3805	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	1.6971	-0.1269	0.0734	1.9511	0.2259	0.9952	0.0591	-0.1283	-0.013	0.526	-0.089	0.6305	-0.0383	-0.1905	0.054	0.8306	-0.0041	0.0004	0.4478	-0.101	0.4242	-25.8167	9.1714	22.2174
2	0.1628	-0.2003	0.032	0.8443	-0.0892	0.9641	0.0528	-0.0142	0.132	-0.6267	-0.1726	0.5183	-0.3821	-0.1608	0.1057	1.2597	0.1844	-0.3536	0.45	-0.0871	0.4892	-20.6774	22.9654	-2.2709
3	0.3594	0.1497	-0.3929	2.9314	0.7936	0.753	-0.1497	0.0251	0.1616	-0.1031	0.0504	-0.0968	-0.2009	0.0193	0.1055	1.0027	0.0985	-0.1946	0.4471	-0.0538	0.3247	-10.6099	19.3329	6.0843
4	0.785	0.1404	0.2218	1.4756	0.2643	0.7988	-0.0945	-0.0088	0.3045	-0.0131	-0.0727	-0.2336	-0.2427	0.1325	0.1395	1.2137	0.0963	-0.2363	0.3657	-0.0564	0.4726	-1.3965	43.0397	16.2779
5	0.614	0.1203	0.0592	0.7227	0.5841	1.6845	-0.0802	-0.1724	-0.3198	0.7488	-0.0668	-0.399	0.1895	0.0241	-0.1769	1.3964	0.0272	-0.3585	0.375	-0.0272	0.2404	3.5013	-18.2233	23.3937
6	0.6429	-0.1575	-0.4048	1.3691	0.3542	0.9585	0.0313	0.0271	-0.0783	0.3846	0.1791	-1.0583	0.2034	0.2559	-0.2076	0.8408	0.1203	-0.4176	0.4763	-0.1455	1.0353	31.5474	-14.6184	13.705
7	0.8057	0.1179	-0.0543	0.7084	0.8851	1.6108	-0.1758	0.0609	0.1123	-0.0867	-0.0367	0.2231	-0.1595	-0.1524	0.1634	1.2772	0.0699	-0.3782	0.5523	-0.2299	0.5708	-32.189	-18.5849	-19.3291
8	0.7893	0.1705	0.4392	0.6725	-0.0585	0.3647	-0.1559	0.0813	0.0211	-0.3234	-0.0456	0.1704	-0.154	-0.041	0.0963	1.0781	0.052	-0.282	0.4515	-0.114	0.3759	-18.7318	-16.3738	-14.9282
9	1.9017	0.155	-0.0775	0.81	0.1047	2.5059	0.0909	0.5576	-0.383	-0.5029	0.0505	-0.3073	0.1141	0.0474	-0.078	1.0574	0.0539	-0.0372	0.5102	-0.22	0.513	9.1689	-33.0486	-13.1165
10	0.5582	-0.1116	0.8968	0.0599	-0.2041	2.839	-0.0306	0.2371	-0.0082	-0.9094	-0.1273	-0.1791	-0.3186	0.1888	-0.0141	1.4036	-0.0338	-0.034	0.5622	-0.0628	0.33	-0.3258	-14.92	-27.232
11	2.3479	-0.82	-0.8058	2.4011	2.1874	4.9655	-0.0305	0.0573	0.4756	-0.9058	-0.1657	-0.0013	-1.1561	0.1037	0.171	0.9335	-0.0923	-0.1505	0.4675	-0.1084	0.2715	-3.2456	-7.058	-14.1519
12	0.845	-0.2376	0.7499	0.3629	-0.9376	2.4563	-0.228	0.4344	0.4103	-0.5058	0.0455	0.1152	-0.9736	-0.1031	0.196	1.8696	0.006	-0.3166	0.7001	-0.0087	0.5885	-9.1902	0.6995	-34.2931
13	0.9378	-0.0626	-0.0703	0.0013	0.0002	0.035	-0.0926	0.2238	0.228	-0.5012	-0.0962	0.0631	-0.3265	0.0322	0.1501	2.2217	0.0225	-0.4654	0.8551	0.1239	0.6861	-16.934	6.6576	-44.1903
14	0.8077	-0.3527	0.5409	0.5502	-0.964	1.664	0.228	0.7972	0.3607	-0.662	-0.3604	-0.3673	-0.4239	0.4613	0.1094	2.337	-0.1027	0.0039	1.1102	0.0668	0.4023	1.7745	-1.044	-51.4172
15	0.2671	0.2068	0.193	0.4993	0.6254	1.453	-0.0763	0.1579	0.245	-0.7582	0.0621	-0.0146	-0.336	-0.048	0.1228	1.468	0.0051	-0.2123	0.4006	-0.1027	0.1932	-58.212	52.6229	-48.2913
16	0.8682	0.3783	0.6706	2.2018	0.5392	0.823	-0.0855	0.0644	-0.0044	-0.4314	0.2797	-0.8668	-0.1821	0.2327	-0.2088	0.785	-0.0539	0.1189	0.4752	-0.1875	0.6014	-30.3876	49.0606	-38.8562
17	0.9471	1.1354	0.1247	1.9621	0.2066	1.2217	0.1209	0.1702	-0.0317	-0.728	-0.0401	1.0084	-0.1125	-0.3885	0.018	0.9345	0.0458	-0.4699	0.597	-0.0625	0.7715	33.3504	21.7593	-53.4049
18	1.0421	0.2702	-0.1843	2.4383	0.4493	2.5581	0.1197	0.035	-0.0466	0.0084	-0.1477	1.0433	0.1676	-0.2369	0.043	0.6238	0.0213	-0.0397	0.3751	-0.0617	0.6526	37.5076	21.9493	-31.9815
19	1.2994	-0.5389	-0.4302	3.2037	0.6652	1.8116	-0.1648	-0.0637	-0.166	0.2609	0.0208	0.3924	0.2385	0.039	0.1395	0.8515	-0.0512	-0.0409	0.3646	0.0257	0.4173	50.8031	8.0472	-31.478
20	1.3009	-0.5136	0.1091	2.4635	-0.0377	1.4741	-0.1189	-0.0257	-0.396	0.0273	0.0072	0.085	0.4322	0.3285	0.1074	1.2229	0.0847	-0.0493	0.4254	0.0136	0.4753	60.4531	-12.3274	-40.6691
21	1.1041	0.687	-0.1471	2.0883	0.4798	1.0553	-0.0863	-0.2689	0.3186	0.6953	-0.033	0.684	-0.0958	-0.0822	0.1202	1.0227	0.1179	0.1249	0.4686	-0.0904	0.5443	45.852	54.7901	-9.3119
22	0.599	0.0565	0.0185	0.3097	0.0235	1.3937	0.0413	-0.3386	-0.1876	0.8911	-0.1261	0.0555	0.4584	0.0789	0.0714	1.5439	0.0917	-0.0206	0.6688	-0.0389	0.3231	61.165	45.4966	-0.2209
23	0.7987	-0.1681	-0.0363	0.1536	-0.0932	1.5171	0.148	-0.5003	-0.3479	0.858	-0.2532	0.1863	0.5206	0.0272	0.0919	2.4526	-0.0265	0.1928	0.9842	0.1205	0.5565	54.8998	33.6825	23.6303

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 184 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 185 through 390 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 391 through 490 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 491 through 797 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 24 through 291 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 292 through 798 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 23 through 81 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 82 through 239 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 240 through 291 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 292 through 433 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 434 through 490 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 491 through 580 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 581 through 648 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 649 through 796 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 23 through 291 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 292 through 795 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 24 through 83 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 84 through 291 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 292 through 580 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 581 through 797 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 24 through 291 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 292 through 552 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 553 through 796 )

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