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

ID or keywords:

Entry

Database: PDB / ID: 9npl

Title

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P1 at 2.25 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: 2.25 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 - E553Q Mutant) from the GH2 family in the space group P1 at 2.25 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	9npl.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb9npl.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	9npl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9npl_validation.pdf.gz	542.4 KB	Display	wwPDB validaton report
Full document	9npl_full_validation.pdf.gz	597.8 KB	Display
Data in XML	9npl_validation.xml.gz	177.7 KB	Display
Data in CIF	9npl_validation.cif.gz	230.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9npl ftp://data.pdbj.org/pub/pdb/validation_reports/np/9npl	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

551 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
276 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Glycoside hydrolase family 2

E: Glycoside hydrolase family 2

hetero molecules

F: Glycoside hydrolase family 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	122.978, 124.405, 133.484
Angle α, β, γ (deg.)	89.21, 117.47, 103.29
Int Tables number	1
Space group name H-M	P1

#1: Protein	Glycoside hydrolase family 2 Mass: 90815.602 Da / Num. of mol.: 6 / Mutation: E553Q 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.: 30 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1156 / 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: 3.22 Å³/Da / Density % sol: 61.77 %
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: 2.25→48.39 Å / Num. obs: 312213 / % possible obs: 95.2 % / Redundancy: 3.51 % / CC_1/2: 0.994 / R_merge(I) obs: 0.091 / R_rim(I) all: 0.108 / Net I/σ(I): 4.71

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.25-2.39	1.17	18702	0.233	1.017	1
2.39-2.55	0.617	17410	0.436	0.873	1
2.55-2.75	0.396	16953	0.721	0.561	1
2.75-3.02	0.225	15016	0.875	0.318	1
3.02-3.37	0.122	12498	0.972	0.173	1
3.37-3.89	0.06	10918	0.989	0.085	1
3.89-4.75	0.051	8920	0.991	0.072	1
4.75-6.69	0.044	6261	0.994	0.062	1
6.69-48.39	0.032	3346	0.995	0.045	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: 2.25→47.41 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2597	15609	5 %
R_work	0.2303	-	-
obs	0.2318	312107	96.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.25→47.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34860	0	338	1156	36354

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	36013
X-RAY DIFFRACTION	f_angle_d	0.538	48797
X-RAY DIFFRACTION	f_dihedral_angle_d	12.6	13094
X-RAY DIFFRACTION	f_chiral_restr	0.044	5129
X-RAY DIFFRACTION	f_plane_restr	0.006	6307

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 (%)
2.25-2.28	0.3484	515	0.3235	9783	X-RAY DIFFRACTION	95
2.28-2.3	0.3579	515	0.3142	9771	X-RAY DIFFRACTION	95
2.3-2.33	0.34	507	0.3054	9643	X-RAY DIFFRACTION	95
2.33-2.36	0.3303	516	0.3014	9788	X-RAY DIFFRACTION	96
2.36-2.39	0.3499	515	0.3024	9787	X-RAY DIFFRACTION	95
2.39-2.42	0.3366	512	0.2936	9740	X-RAY DIFFRACTION	96
2.42-2.46	0.3058	516	0.2813	9808	X-RAY DIFFRACTION	96
2.46-2.49	0.3382	513	0.2856	9741	X-RAY DIFFRACTION	96
2.49-2.53	0.3239	517	0.2793	9820	X-RAY DIFFRACTION	96
2.53-2.58	0.2914	515	0.2704	9791	X-RAY DIFFRACTION	96
2.58-2.62	0.3097	520	0.271	9869	X-RAY DIFFRACTION	96
2.62-2.67	0.3159	519	0.2729	9869	X-RAY DIFFRACTION	96
2.67-2.72	0.2887	518	0.2725	9835	X-RAY DIFFRACTION	97
2.72-2.77	0.3183	521	0.2735	9883	X-RAY DIFFRACTION	97
2.77-2.83	0.309	518	0.2637	9840	X-RAY DIFFRACTION	97
2.83-2.9	0.2887	523	0.2552	9942	X-RAY DIFFRACTION	97
2.9-2.97	0.287	520	0.2534	9861	X-RAY DIFFRACTION	97
2.97-3.05	0.2818	520	0.2542	9896	X-RAY DIFFRACTION	97
3.05-3.14	0.2761	524	0.2477	9938	X-RAY DIFFRACTION	97
3.14-3.24	0.287	523	0.2504	9933	X-RAY DIFFRACTION	97
3.24-3.36	0.2752	522	0.2474	9920	X-RAY DIFFRACTION	97
3.36-3.5	0.2703	526	0.2314	10005	X-RAY DIFFRACTION	98
3.5-3.65	0.2596	527	0.2209	10003	X-RAY DIFFRACTION	98
3.65-3.85	0.2229	525	0.2117	9976	X-RAY DIFFRACTION	98
3.85-4.09	0.2229	525	0.1997	9966	X-RAY DIFFRACTION	98
4.09-4.4	0.2251	528	0.1881	10041	X-RAY DIFFRACTION	98
4.4-4.85	0.2077	525	0.1819	9964	X-RAY DIFFRACTION	98
4.85-5.55	0.2178	522	0.1935	9913	X-RAY DIFFRACTION	97
5.55-6.98	0.2472	529	0.213	10065	X-RAY DIFFRACTION	98
6.98-47.41	0.2181	533	0.2071	10107	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	0.4372	-0.2086	-0.1432	1.4042	0.595	1.0157	-0.0342	-0.0318	-0.1289	0.1506	-0.0246	0.0103	0.2097	-0.0584	0.0713	0.3808	-0.0168	-0.0104	0.2972	0.0088	0.309	-85.0192	-27.823	-21.1588
2	1.2716	-0.4262	-0.3874	1.213	0.4822	1.1269	-0.0096	0.1203	-0.0601	-0.1582	0.0392	-0.172	0.0376	0.1188	-0.0714	0.2903	-0.018	-0.0179	0.2578	0.0188	0.2813	-67.9985	-18.6274	-28.9388
3	1.3577	0.0932	-0.1705	1.489	0.1925	0.7788	0.012	0.0044	-0.2431	-0.1959	0.0882	-0.7487	0.1408	0.4099	-0.1075	0.3567	0.0547	0.0451	0.5131	-0.0286	0.648	-45.6763	-30.1635	-34.6159
4	0.4777	-0.0969	0.2211	0.9254	-0.0548	1.0856	0.046	-0.0488	-0.0636	0.0056	0.0017	0.2641	0.0532	-0.2297	-0.0578	0.2432	-0.022	-0.0298	0.3003	0.0129	0.3238	-112.527	1.4251	-26.094
5	0.5378	0.1235	0.3033	1.0473	0.2511	0.9265	-0.0259	0.0468	0.0735	-0.1093	-0.0117	0.0044	-0.17	0.0438	0.0274	0.301	0.0305	-0.0343	0.2507	0.0127	0.2891	-97.5389	24.4824	-36.6267
6	0.6853	-0.3493	0.0697	1.3121	0.1964	0.3739	-0.0116	0.1664	-0.0832	-0.208	-0.0618	0.2005	0.0837	-0.0127	0.0659	0.4768	-0.0181	-0.0818	0.3192	-0.0556	0.3439	-105.0171	-30.3282	-60.3177
7	1.072	-0.4697	0.305	1.366	-0.4575	1.2799	0.0655	0.4347	0.2595	-0.6116	-0.1676	-0.0752	-0.178	0.0861	0.1061	0.8144	-0.0074	-0.0357	0.5196	0.0461	0.3881	-93.0492	-14.5107	-82.2279
8	0.5348	0.1801	0.1994	1.5787	0.4647	0.9793	-0.0386	0.0468	0.1256	-0.1676	-0.0213	0.0992	-0.1804	-0.0699	0.0772	0.3215	-0.0036	0.0006	0.278	-0.0021	0.2602	-84.8774	29.6749	23.6061
9	0.815	0.2334	0.1872	1.2805	0.2697	0.9027	0.0125	-0.0472	0.0602	0.1489	0.0617	-0.3917	-0.0767	0.2867	-0.0833	0.3026	-0.0161	-0.0271	0.3654	-0.0194	0.3808	-56.5685	26.5211	34.497
10	0.5424	0.1422	-0.365	0.6727	0.0429	1.2099	0.035	0.0014	0.0338	0.0406	-0.0346	0.2903	-0.0153	-0.2199	-0.0235	0.2446	0.003	0.02	0.3134	-0.0051	0.3459	-113.7618	-0.501	35.8111
11	0.6648	-0.2208	-0.3264	1.0917	0.1541	1.2398	-0.0658	-0.0749	-0.1007	0.0383	0.0295	-0.0316	0.2204	0.1538	0.0263	0.2928	-0.0207	0.0176	0.2845	0.0257	0.3026	-95.183	-24.302	36.8072
12	1.1668	0.8496	-0.3037	1.5399	0.1056	0.3815	0.0735	-0.1994	0.2152	0.2801	-0.0946	0.3452	-0.1134	-0.0533	-0.0058	0.4304	0.0145	0.0876	0.3748	-0.0597	0.3835	-43.3446	45.1902	-54.7197
13	1.0826	0.515	-0.329	1.3242	-0.3709	1.2437	0.1469	-0.5103	-0.2387	0.775	-0.2508	0.0071	0.1306	0.0769	0.1242	0.8892	-0.0756	0.0358	0.6185	0.0418	0.4116	-31.5383	29.489	-32.2933

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 291 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 292 through 568 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 569 through 798 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 24 through 239 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 240 through 798 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 24 through 291 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 292 through 798 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 15 through 291 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 292 through 798 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 24 through 291 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 292 through 798 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 23 through 291 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 292 through 798 )

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