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

ID or keywords:

Entry

Database: PDB / ID: 9npc

Title

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group I212121 at 2.65 A

Components

Glycoside hydrolase family 2

Keywords

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

Function / homology

DI(HYDROXYETHYL)ETHER / PHOSPHATE ION

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 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 I212121 at 2.65 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	9npc.cif.gz	900.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9npc.ent.gz	755.3 KB	Display	PDB format
PDBx/mmJSON format	9npc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9npc_validation.pdf.gz	477.1 KB	Display	wwPDB validaton report
Full document	9npc_full_validation.pdf.gz	493.1 KB	Display
Data in XML	9npc_validation.xml.gz	86.8 KB	Display
Data in CIF	9npc_validation.cif.gz	115.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9npc ftp://data.pdbj.org/pub/pdb/validation_reports/np/9npc	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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, electron microscopy

Unit cell

Length a, b, c (Å)	191.853, 192.001, 191.921
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

#1: Protein	Glycoside hydrolase family 2 Mass: 91895.203 Da / Num. of mol.: 3 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.: 11 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 434 / 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: 3.21 Å³/Da / Density % sol: 61.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1 M ammonium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, 0.1 M praseodyminium

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97934 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 2.65→48 Å / Num. obs: 102548 / % possible obs: 99.7 % / Redundancy: 7.06 % / CC_1/2: 0.989 / R_merge(I) obs: 0.163 / R_rim(I) all: 0.176 / Net I/σ(I): 4.6

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.65-2.81	1.361	19539	0.244	1.916	1
2.81-3	0.827	18600	0.414	1.166	1
3-3.24	0.472	17209	0.69	0.665	1
3.24-3.55	0.249	15195	0.882	0.351	1
3.55-3.97	0.125	14416	0.96	0.176	1
3.97-4.58	0.07	12321	0.987	0.099	1
4.58-5.59	0.055	10179	0.992	0.078	1
5.59-7.85	0.045	8084	0.994	0.064	1
7.85-48	0.024	4380	0.997	0.034	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: 2.65→45.25 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2329	5115	5 %
R_work	0.2026	-	-
obs	0.2041	102256	99.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.65→45.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17752	0	176	434	18362

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	18393
X-RAY DIFFRACTION	f_angle_d	0.763	24927
X-RAY DIFFRACTION	f_dihedral_angle_d	13.907	6745
X-RAY DIFFRACTION	f_chiral_restr	0.055	2611
X-RAY DIFFRACTION	f_plane_restr	0.012	3227

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 (%)
2.65-2.68	0.3621	167	0.3317	3142	X-RAY DIFFRACTION	96
2.68-2.71	0.3235	166	0.2935	3157	X-RAY DIFFRACTION	100
2.71-2.74	0.3365	169	0.2812	3204	X-RAY DIFFRACTION	100
2.75-2.78	0.3351	171	0.281	3249	X-RAY DIFFRACTION	100
2.78-2.82	0.3501	170	0.2861	3248	X-RAY DIFFRACTION	100
2.82-2.85	0.3446	166	0.2857	3140	X-RAY DIFFRACTION	100
2.85-2.9	0.3223	171	0.299	3249	X-RAY DIFFRACTION	100
2.9-2.94	0.3277	169	0.2939	3210	X-RAY DIFFRACTION	100
2.94-2.98	0.3554	170	0.2996	3232	X-RAY DIFFRACTION	100
2.98-3.03	0.3886	171	0.2836	3247	X-RAY DIFFRACTION	100
3.03-3.09	0.336	169	0.2698	3218	X-RAY DIFFRACTION	100
3.09-3.14	0.2863	169	0.2546	3202	X-RAY DIFFRACTION	100
3.14-3.2	0.3147	170	0.2531	3236	X-RAY DIFFRACTION	100
3.2-3.27	0.2993	168	0.2447	3187	X-RAY DIFFRACTION	100
3.27-3.34	0.2531	169	0.2392	3208	X-RAY DIFFRACTION	100
3.34-3.42	0.2676	169	0.244	3223	X-RAY DIFFRACTION	100
3.42-3.5	0.2737	170	0.2455	3221	X-RAY DIFFRACTION	100
3.5-3.6	0.2402	170	0.2013	3230	X-RAY DIFFRACTION	100
3.6-3.7	0.2602	174	0.2193	3303	X-RAY DIFFRACTION	100
3.7-3.82	0.2153	166	0.1878	3164	X-RAY DIFFRACTION	100
3.82-3.96	0.2047	172	0.1781	3256	X-RAY DIFFRACTION	100
3.96-4.12	0.2046	172	0.1692	3270	X-RAY DIFFRACTION	100
4.12-4.3	0.2018	171	0.161	3240	X-RAY DIFFRACTION	100
4.3-4.53	0.1935	171	0.1535	3257	X-RAY DIFFRACTION	100
4.53-4.81	0.1738	171	0.1567	3256	X-RAY DIFFRACTION	100
4.81-5.19	0.1726	172	0.1572	3257	X-RAY DIFFRACTION	100
5.19-5.71	0.1889	171	0.1708	3259	X-RAY DIFFRACTION	100
5.71-6.53	0.2083	176	0.1849	3334	X-RAY DIFFRACTION	100
6.53-8.22	0.1938	175	0.1753	3321	X-RAY DIFFRACTION	100
8.23-45.25	0.1833	180	0.1774	3421	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	2.0358	-1.0945	-0.8077	2.4281	0.6805	1.3416	-0.0727	-0.1588	-0.3201	0.1935	0.0589	0.0387	0.2448	-0.05	0.0247	0.4414	-0.0399	-0.0551	0.3709	0.0465	0.398	40.7895	18.7999	-30.2076
2	1.6908	-0.0583	-0.5197	0.9409	0.3099	1.6849	-0.0003	0.1762	-0.0911	-0.0814	-0.0726	0.1804	-0.0242	-0.2918	0.0698	0.3779	-0.0185	-0.016	0.3598	-0.0065	0.4437	33.9714	24.2253	-55.0751
3	2.7436	-0.9089	0.1408	1.5986	-0.794	1.3675	0.1294	-0.1421	-0.1383	0.1953	0.0531	0.5668	-0.0428	-0.4385	-0.1357	0.4546	-0.0336	0.0177	0.5142	-0.0677	0.6345	6.844	32.3006	-47.7609
4	2.1823	0.4065	0.8353	1.4196	0.8461	2.2569	0.0505	-0.0177	-0.1728	-0.0581	0.0088	-0.1769	0.1274	0.2963	-0.078	0.3507	0.0487	0.0413	0.3984	0.0521	0.4306	77.1619	30.2299	-55.1291
5	0.7935	0.2145	-0.0588	1.5238	0.6643	1.7504	-0.0714	0.1956	0.0415	-0.2511	0.1074	-0.0063	-0.2146	0.1229	-0.0108	0.3671	-0.0122	0.0091	0.4551	0.0191	0.4084	71.7397	55.1036	-61.9864
6	1.5475	-0.762	0.7499	1.1371	0.0996	2.5206	0.0682	0.5216	-0.1971	-0.3789	-0.2014	0.0753	0.1605	0.0498	0.1104	0.5265	-0.0746	0.0173	0.6505	-0.01	0.4702	63.6522	47.753	-89.1021
7	1.5289	1.0344	-0.6376	2.3865	-1.0353	1.8439	0.0287	-0.1272	0.018	0.3144	-0.0646	-0.1278	0.0089	0.1378	0.0628	0.3722	0.055	-0.0466	0.402	-0.0452	0.3074	65.7164	55.1821	-18.7792
8	1.7309	0.6589	-0.4022	1.9386	0.1204	0.92	0.097	0.0011	0.258	0.1169	-0.0253	0.2194	-0.1952	-0.0601	-0.0672	0.431	0.024	-0.0015	0.3857	-0.0023	0.3496	40.837	62.0197	-24.2195
9	1.1555	0.0605	0.6539	2.5778	-0.9923	1.501	-0.1567	0.0679	0.337	0.0986	0.1004	-0.1666	-0.5163	0.2154	0.03	0.5856	-0.0115	0.0648	0.4179	-0.0358	0.4755	48.1897	89.163	-32.2796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 184 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 185 through 451 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 452 through 796 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 19 through 184 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 185 through 451 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 452 through 796 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 19 through 184 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 185 through 451 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 452 through 796 )

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