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

ID or keywords:

Entry

Database: PDB / ID: 9npd

Title

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P3121 at 3.05 A

Components

Glycoside hydrolase family 2

Keywords

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

Function / homology

ACETATE ION / MALONATE ION / PHOSPHATE ION

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.05 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 P3121 at 3.05 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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PDBx/mmCIF format	9npd.cif.gz	899.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9npd.ent.gz	757.4 KB	Display	PDB format
PDBx/mmJSON format	9npd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9npd_validation.pdf.gz	492.5 KB	Display	wwPDB validaton report
Full document	9npd_full_validation.pdf.gz	510.4 KB	Display
Data in XML	9npd_validation.xml.gz	87.3 KB	Display
Data in CIF	9npd_validation.cif.gz	108.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9npd ftp://data.pdbj.org/pub/pdb/validation_reports/np/9npd	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

274 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)	222.906, 222.906, 151.360
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Glycoside hydrolase family 2 Mass: 90815.602 Da / Num. of mol.: 3 / 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.: 10 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.98 Å³/Da / Density % sol: 69.13 %
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 malonate

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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: 3.05→49.02 Å / Num. obs: 82584 / % possible obs: 99.9 % / Redundancy: 19.72 % / CC_1/2: 0.982 / R_merge(I) obs: 0.241 / R_rim(I) all: 0.297 / Net I/σ(I): 3.24

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
3.05-3.23	2.713	12530	0.212	3.356	1
3.23-3.46	1.422	11455	0.454	1.765	1
3.46-3.73	0.732	11071	0.752	0.908	1
3.73-4.09	0.425	10163	0.902	0.52	1
4.09-4.56	0.243	8966	0.956	0.299	1
4.56-5.26	0.178	7635	0.967	0.22	1
5.26-6.43	0.156	6274	0.972	0.192	1
6.43-9.01	0.083	4825	0.99	0.101	1
9.01-49.02	0.052	2710	0.993	0.063	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: 3.05→49.02 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2385	4125	5 %
R_work	0.2175	-	-
obs	0.2186	82474	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.05→49.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17763	0	76	71	17910

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	18287
X-RAY DIFFRACTION	f_angle_d	0.705	24830
X-RAY DIFFRACTION	f_dihedral_angle_d	11.643	6655
X-RAY DIFFRACTION	f_chiral_restr	0.053	2611
X-RAY DIFFRACTION	f_plane_restr	0.013	3230

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 (%)
3.05-3.09	0.483	138	0.4493	2627	X-RAY DIFFRACTION	97
3.09-3.12	0.4286	139	0.4114	2655	X-RAY DIFFRACTION	100
3.12-3.16	0.443	142	0.3804	2690	X-RAY DIFFRACTION	100
3.16-3.2	0.4106	141	0.3812	2672	X-RAY DIFFRACTION	100
3.2-3.25	0.3896	140	0.357	2671	X-RAY DIFFRACTION	100
3.25-3.29	0.4181	143	0.3319	2709	X-RAY DIFFRACTION	100
3.29-3.34	0.3789	140	0.3365	2658	X-RAY DIFFRACTION	100
3.34-3.4	0.3364	140	0.3209	2658	X-RAY DIFFRACTION	100
3.4-3.45	0.3349	144	0.3142	2737	X-RAY DIFFRACTION	100
3.45-3.51	0.3308	141	0.302	2692	X-RAY DIFFRACTION	100
3.51-3.58	0.3123	140	0.2702	2644	X-RAY DIFFRACTION	100
3.58-3.64	0.3173	143	0.2508	2720	X-RAY DIFFRACTION	100
3.64-3.72	0.2226	141	0.2442	2676	X-RAY DIFFRACTION	100
3.72-3.8	0.2562	142	0.2245	2701	X-RAY DIFFRACTION	100
3.8-3.89	0.2331	141	0.215	2668	X-RAY DIFFRACTION	100
3.89-3.98	0.2361	143	0.2012	2719	X-RAY DIFFRACTION	100
3.98-4.09	0.2415	141	0.1999	2681	X-RAY DIFFRACTION	100
4.09-4.21	0.208	142	0.1903	2703	X-RAY DIFFRACTION	100
4.21-4.35	0.1817	142	0.1915	2690	X-RAY DIFFRACTION	100
4.35-4.5	0.2155	142	0.1846	2694	X-RAY DIFFRACTION	100
4.5-4.68	0.2086	142	0.1762	2704	X-RAY DIFFRACTION	100
4.68-4.9	0.1705	144	0.1595	2727	X-RAY DIFFRACTION	100
4.9-5.15	0.2058	142	0.1742	2701	X-RAY DIFFRACTION	100
5.16-5.48	0.1999	142	0.1849	2709	X-RAY DIFFRACTION	100
5.48-5.9	0.2287	144	0.1953	2723	X-RAY DIFFRACTION	100
5.9-6.49	0.1911	144	0.2008	2749	X-RAY DIFFRACTION	100
6.49-7.43	0.2066	145	0.2012	2746	X-RAY DIFFRACTION	100
7.43-9.35	0.1889	146	0.1665	2769	X-RAY DIFFRACTION	100
9.35-49.02	0.1983	151	0.1868	2856	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	4.2029	-2.1795	-1.5025	1.2756	-0.1209	4.8709	0.048	-0.2252	-0.2594	-0.0247	0.0777	0.3915	0.1599	-0.8553	-0.2054	0.4761	-0.1587	0.0468	0.7587	0.0019	1.5351	41.138	-48.991	28.25
2	0.9506	0.4909	0.0694	2.0429	0.808	0.9838	0.0024	0.0807	-0.1084	0.1245	-0.0519	0.4124	0.0691	-0.2386	0.0564	0.4673	-0.0589	0.0717	0.5458	0.0679	1.3642	56.084	-34.901	35.232
3	1.3003	0.3928	1.7463	2.538	-0.5233	6.184	-0.1271	0.2802	0.0654	0.0897	0.0725	-0.2374	0.2996	0.4526	0.0681	0.512	-0.012	0.0281	0.4638	0.0488	1.4864	70.427	-44.411	37.367
4	2.0594	0.6925	0.6406	2.628	-0.119	1.8159	0.1791	-0.0563	-0.7926	0.4695	-0.0111	-0.45	0.8001	0.1322	-0.1802	0.9908	0.0491	-0.0298	0.552	0.084	1.7181	74.575	-66.925	49.12
5	0.7475	-0.187	-0.7462	1.0108	0.7944	2.6212	0.1313	0.1434	0.2974	-0.5249	0.0032	-0.071	-0.6696	-0.1142	-0.1454	0.7987	0.0032	0.0775	0.4808	0.1087	1.3748	70.915	-5.846	6.233
6	1.9065	-0.7542	0.2506	2.0083	2.2878	3.1937	0.1685	-0.336	-0.1717	0.1758	0.083	-0.0136	0.1113	0.2859	-0.2321	0.6581	-0.1219	0.1411	0.5909	-0.0143	1.4176	86.715	-10.599	18.248
7	2.8733	-0.6047	-0.8965	1.113	1.19	2.0536	0.0422	-0.4434	0.4816	-0.095	0.5061	-0.7952	-0.4505	0.9871	-0.5507	0.8456	-0.2634	0.1863	0.95	-0.2725	1.826	96.578	6.343	34.576
8	0.5217	0.2218	-0.0955	2.3616	-1.209	2.4471	-0.0816	0.1704	0.0258	-0.1272	0.1928	0.506	-0.026	-0.5962	-0.1283	0.5311	-0.0291	0.0275	0.6629	-0.0805	1.013	66.301	-40.497	-13.876
9	5.263	-1.3328	-3.4192	2.0074	-0.4501	3.4139	-0.1548	0.2978	-0.7201	0.0104	-0.0851	-0.029	0.4497	-0.0467	0.2439	0.6427	-0.0748	0.0116	0.5192	-0.1123	1.3659	73.576	-65.523	4.944
10	1.5652	-0.1917	-0.8306	0.5981	-0.5145	2.1757	0.0576	0.0857	-0.0676	-0.3752	-0.0318	-0.556	-0.0696	0.4871	-0.0157	0.6834	-0.1039	0.2087	0.6613	-0.1439	1.4074	97.876	-49.474	-13.958

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 20:81 )	A	20 - 81
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 82:329 )	A	82 - 329
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 330:499 )	A	330 - 499
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 500:797 )	A	500 - 797
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 23:329 )	B	23 - 329
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 330:540 )	B	330 - 540
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 541:797 )	B	541 - 797
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 24:239 )	C	24 - 239
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 240:349 )	C	240 - 349
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 350:797 )	C	350 - 797

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