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

ID or keywords:

Entry

Database: PDB / ID: 9npe

Title

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group P1 at 2.40 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: 2.4 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) from the GH2 family in the space group P1 at 2.40 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	9npe.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb9npe.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	9npe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9npe_validation.pdf.gz	529.8 KB	Display	wwPDB validaton report
Full document	9npe_full_validation.pdf.gz	574.7 KB	Display
Data in XML	9npe_validation.xml.gz	194.3 KB	Display
Data in CIF	9npe_validation.cif.gz	258.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9npe ftp://data.pdbj.org/pub/pdb/validation_reports/np/9npe	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

557 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
278 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Glycoside hydrolase family 2

F: Glycoside hydrolase family 2

hetero molecules

E: Glycoside hydrolase family 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	122.520, 124.140, 133.600
Angle α, β, γ (deg.)	89.30, 117.29, 103.48
Int Tables number	1
Space group name H-M	P1

#1: Protein	Glycoside hydrolase family 2 Mass: 91895.203 Da / Num. of mol.: 6 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.: 26 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2204 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.17 Å³/Da / Density % sol: 61.15 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.75 M ammonium phosphate dibasic, 0.1 M imidazole, pH8, 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

/ Beamline: W01B-MX2 / Wavelength: 0.97822 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97822 Å / Relative weight: 1

Reflection

Resolution: 2.4→20 Å / Num. obs: 264442 / % possible obs: 99 % / Redundancy: 5.1 % / CC_1/2: 0.995 / R_merge(I) obs: 0.136 / R_rim(I) all: 0.152 / Net I/σ(I): 8.56

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.4-2.46	0.981	39020	0.685	1.104	1
2.46-2.53	0.912	38193	0.751	1.013	1
2.53-2.6	0.76	37003	0.828	0.841	1
2.6-2.68	0.646	35972	0.868	0.715	1
2.68-2.77	0.527	34952	0.904	0.584	1
2.77-2.87	0.425	33545	0.931	0.471	1
2.87-2.98	0.338	32648	0.953	0.375	1
2.98-3.1	0.27	31203	0.968	0.301	1
3.1-3.24	0.208	29932	0.978	0.233	1
3.24-3.39	0.153	28635	0.985	0.173	1
3.39-3.58	0.124	27088	0.989	0.139	1
3.58-3.79	0.102	25595	0.993	0.115	1
3.79-4.06	0.086	23906	0.994	0.096	1
4.06-4.38	0.074	22076	0.995	0.083	1
4.38-4.8	0.067	20282	0.995	0.075	1
4.8-5.37	0.068	18378	0.995	0.076	1
5.37-6.2	0.072	16349	0.994	0.082	1
6.2-7.59	0.063	13910	0.996	0.071	1
7.59-10.73	0.046	10649	0.998	0.051	1
10.73-20	0.042	4912	0.998	0.047	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: 2.4→20 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2553	13173	5 %
R_work	0.2223	-	-
obs	0.224	263465	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	35095	0	334	2204	37633

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	36277
X-RAY DIFFRACTION	f_angle_d	0.546	49188
X-RAY DIFFRACTION	f_dihedral_angle_d	13.305	13188
X-RAY DIFFRACTION	f_chiral_restr	0.044	5156
X-RAY DIFFRACTION	f_plane_restr	0.004	6345

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 (%)
2.4-2.43	0.3269	439	0.2827	8338	X-RAY DIFFRACTION	100
2.43-2.46	0.3304	436	0.2883	8285	X-RAY DIFFRACTION	100
2.46-2.49	0.3113	444	0.2809	8431	X-RAY DIFFRACTION	100
2.49-2.52	0.3498	439	0.2763	8331	X-RAY DIFFRACTION	100
2.52-2.55	0.3239	440	0.2719	8365	X-RAY DIFFRACTION	100
2.55-2.58	0.2942	440	0.2538	8355	X-RAY DIFFRACTION	100
2.58-2.62	0.3219	441	0.2614	8361	X-RAY DIFFRACTION	100
2.62-2.66	0.3058	438	0.255	8330	X-RAY DIFFRACTION	100
2.66-2.7	0.3128	440	0.2537	8357	X-RAY DIFFRACTION	100
2.7-2.75	0.3229	438	0.2542	8335	X-RAY DIFFRACTION	100
2.75-2.79	0.2785	441	0.2472	8368	X-RAY DIFFRACTION	100
2.79-2.84	0.3112	442	0.2542	8391	X-RAY DIFFRACTION	100
2.84-2.9	0.2944	436	0.2458	8300	X-RAY DIFFRACTION	100
2.9-2.96	0.2945	441	0.241	8377	X-RAY DIFFRACTION	100
2.96-3.02	0.3031	439	0.2523	8342	X-RAY DIFFRACTION	100
3.02-3.09	0.3002	438	0.2436	8312	X-RAY DIFFRACTION	100
3.09-3.17	0.2819	441	0.2425	8382	X-RAY DIFFRACTION	100
3.17-3.25	0.3044	440	0.2326	8356	X-RAY DIFFRACTION	100
3.25-3.35	0.2588	437	0.2325	8292	X-RAY DIFFRACTION	100
3.35-3.46	0.2601	439	0.225	8349	X-RAY DIFFRACTION	100
3.46-3.58	0.2443	439	0.2243	8334	X-RAY DIFFRACTION	100
3.58-3.72	0.2409	441	0.2098	8371	X-RAY DIFFRACTION	100
3.72-3.89	0.2555	436	0.2127	8285	X-RAY DIFFRACTION	100
3.89-4.09	0.2361	438	0.2055	8312	X-RAY DIFFRACTION	100
4.09-4.35	0.2087	438	0.194	8322	X-RAY DIFFRACTION	100
4.35-4.68	0.1972	438	0.1864	8320	X-RAY DIFFRACTION	100
4.68-5.14	0.2072	439	0.1876	8364	X-RAY DIFFRACTION	100
5.14-5.87	0.2236	440	0.2048	8348	X-RAY DIFFRACTION	100
5.87-7.34	0.2376	438	0.2165	8355	X-RAY DIFFRACTION	100
7.34-20	0.2225	437	0.2017	8324	X-RAY DIFFRACTION	100

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	0.2605	0.186	-0.081	0.2488	0.0412	0.2236	-0.0283	0.0631	0.066	-0.0418	0.0074	0.0554	-0.0802	-0.0009	-0	0.2301	0.0036	-0.0292	0.1831	-0.0064	0.1759	-18.4576	2.1484	-6.8711
2	0.3108	0.183	0.2062	0.5601	0.1916	0.3427	0.0182	0.0228	0.0021	0.1017	0.0417	-0.1297	-0.0351	0.0477	0	0.1565	-0.0171	-0.0259	0.2299	-0.0137	0.2328	10.0118	-1.3663	3.7893
3	0.0404	0.2267	-0.067	0.452	0.0266	0.1936	0.0252	0.0226	0.0207	0.0227	-0.0091	0.1896	-0.0005	0.0066	-0	0.1224	0.0238	0.0518	0.2625	0.0176	0.2689	-47.2227	-28.2823	4.9172
4	0.0951	-0.0505	-0.0108	0.3571	-0.0438	0.3155	-0.0228	0.0163	0.007	0.0817	0.0128	-0.0138	0.0294	0.071	-0	0.2079	-0.025	0.0574	0.2828	0.0133	0.257	-33.3544	-41.6201	12.1224
5	0.1269	-0.0289	-0.0887	0.372	0.1557	0.1811	-0.0639	0.0462	-0.0797	-0.0227	-0.01	-0.0196	0.193	0.0555	-0	0.3099	0.0496	0.0428	0.2284	0.04	0.2671	-23.8973	-62.1052	-0.4776
6	0.1754	0.0518	-0.1054	0.2727	0.2603	0.2673	0.0058	-0.0773	0.0731	0.3194	-0.0441	0.1679	-0.1024	0.0136	0	0.3011	0.0077	0.1259	0.2672	-0.0269	0.3553	-38.4057	4.5399	32.3565
7	0.5453	0.1273	0.0279	0.2952	-0.1181	0.3291	0.0896	-0.1686	-0.0784	0.3892	-0.1316	0.0268	0.0922	0.0069	-0	0.6594	-0.0808	0.0858	0.33	0.0204	0.1876	-26.4692	-11.4248	54.7456
8	0.2125	-0.202	0.0664	0.2056	-0.0305	0.3231	-0.0085	-0.0418	-0.0514	0.0655	0.0066	0.0144	0.1147	-0.034	-0	0.2255	-0.0279	0.0274	0.1788	-0.0063	0.1904	-18.3166	-55.3984	-52.0674
9	0.3604	-0.1628	-0.1995	0.5634	0.2371	0.3534	0.024	-0.0088	-0.0072	-0.0843	0.0313	-0.1524	0.0382	0.0283	0	0.1326	0.0259	0.0196	0.2072	0.001	0.246	10.1408	-51.7946	-62.7723
10	0.1955	-0.305	0.0541	0.3278	0.0226	0.1724	-0.0241	-0.0406	-0.0499	0.0008	0.0283	0.1094	0.0322	0.0131	-0	0.1066	-0.0259	-0.0189	0.2126	0.0094	0.2211	15.2144	-39.0825	61.126
11	0.2114	0.0793	0.2659	0.5721	0.0826	0.3829	-0.0026	-0.0006	0.0111	-0.0769	-0.0113	-0.0215	-0.1169	0.0104	-0	0.1809	0.0225	-0.0293	0.1631	0.012	0.1907	30.3088	-16.1156	50.6902
12	0.1417	-0.0238	0.085	0.3627	0.2634	0.2715	-0.0115	0.0618	-0.0419	-0.1686	-0.0529	0.0936	0.0632	0.0063	0	0.3273	-0.0124	-0.0731	0.248	-0.0309	0.2856	-38.2799	-57.6844	-91.3201
13	0.5765	-0.1773	0.175	0.3725	-0.0177	0.3333	0.0447	0.1534	0.1279	-0.3826	-0.0804	-0.0435	-0.0877	0.0346	-0	0.5715	0.0088	-0.0372	0.2502	0.0471	0.1566	-26.1648	-41.554	-113.6927

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 797 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 24 through 291 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 292 through 566 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 567 through 797 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 24 through 291 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 292 through 797 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 19 through 291 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 292 through 797 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 24 through 239 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 240 through 797 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 24 through 291 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 292 through 797 )

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