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

ID or keywords:

Entry

Database: PDB / ID: 9npf

Title

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group P1 at 2.15 A

Components

Glycoside hydrolase family 2

Keywords

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

Function / homology

ACETATE ION / PHOSPHATE ION

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 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 2.15 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	9npf.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb9npf.ent.gz	1.5 MB	Display	PDB format
PDBx/mmJSON format	9npf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9npf_validation.pdf.gz	535.1 KB	Display	wwPDB validaton report
Full document	9npf_full_validation.pdf.gz	589 KB	Display
Data in XML	9npf_validation.xml.gz	188.8 KB	Display
Data in CIF	9npf_validation.cif.gz	245.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9npf ftp://data.pdbj.org/pub/pdb/validation_reports/np/9npf	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

554 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
277 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
277 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.703, 123.566, 133.238
Angle α, β, γ (deg.)	89.44, 117.29, 103.20
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.: 14 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1588 / 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: 3.13 Å³/Da / Density % sol: 60.64 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1 M ammonium phosphate dibasic, 0.1 M sodium acetate, pH 4.5

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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: 0.97915 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.97915 Å / Relative weight: 1

Reflection

Resolution: 2.15→49 Å / Num. obs: 344315 / % possible obs: 89.3 % / Redundancy: 3.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.091 / Net I/σ(I): 6.72

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.15-2.28	0.262	52250	0.883	0.371	1
2.28-2.44	0.159	54764	0.932	0.225	1
2.44-2.63	0.118	49864	0.958	0.167	1
2.63-2.88	0.074	44378	0.987	0.105	1
2.88-3.22	0.034	42218	0.996	0.048	1
3.22-3.72	0.022	34847	0.998	0.031	1
3.72-4.55	0.016	30955	0.998	0.022	1
4.55-6.4	0.025	22290	1	0.035	1
6.4-49	0.03	12749			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: 2.15→49 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2279	16355	5 %
R_work	0.2075	-	-
obs	0.2085	327117	90.09 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	35361	0	186	1588	37135

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	36437
X-RAY DIFFRACTION	f_angle_d	0.717	49433
X-RAY DIFFRACTION	f_dihedral_angle_d	13.012	13263
X-RAY DIFFRACTION	f_chiral_restr	0.051	5189
X-RAY DIFFRACTION	f_plane_restr	0.006	6405

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 (%)
2.15-2.17	0.4124	511	0.4177	9839	X-RAY DIFFRACTION	85
2.17-2.2	0.3649	528	0.3346	9992	X-RAY DIFFRACTION	88
2.2-2.23	0.3948	518	0.3458	9788	X-RAY DIFFRACTION	85
2.23-2.25	0.3146	481	0.3214	9135	X-RAY DIFFRACTION	79
2.25-2.28	0.3308	541	0.3065	10270	X-RAY DIFFRACTION	89
2.28-2.32	0.3251	556	0.2924	10548	X-RAY DIFFRACTION	92
2.32-2.35	0.3123	561	0.2906	10655	X-RAY DIFFRACTION	92
2.35-2.38	0.3302	561	0.295	10658	X-RAY DIFFRACTION	92
2.38-2.42	0.3048	558	0.2782	10605	X-RAY DIFFRACTION	92
2.42-2.46	0.3153	556	0.2683	10557	X-RAY DIFFRACTION	92
2.46-2.5	0.3017	551	0.2721	10460	X-RAY DIFFRACTION	91
2.5-2.55	0.3064	551	0.2613	10498	X-RAY DIFFRACTION	91
2.55-2.6	0.2703	546	0.2483	10370	X-RAY DIFFRACTION	90
2.6-2.65	0.2806	542	0.2497	10287	X-RAY DIFFRACTION	89
2.65-2.71	0.2793	525	0.2504	9995	X-RAY DIFFRACTION	87
2.71-2.77	0.2662	498	0.2448	9471	X-RAY DIFFRACTION	82
2.77-2.84	0.2709	564	0.2443	10708	X-RAY DIFFRACTION	93
2.84-2.92	0.2613	563	0.2413	10684	X-RAY DIFFRACTION	93
2.92-3	0.2888	564	0.2393	10727	X-RAY DIFFRACTION	93
3-3.1	0.2334	558	0.2224	10586	X-RAY DIFFRACTION	92
3.1-3.21	0.2396	556	0.2127	10579	X-RAY DIFFRACTION	92
3.21-3.34	0.2317	551	0.2096	10481	X-RAY DIFFRACTION	91
3.34-3.49	0.2283	541	0.2057	10263	X-RAY DIFFRACTION	89
3.49-3.68	0.2022	518	0.1878	9853	X-RAY DIFFRACTION	86
3.68-3.91	0.2048	573	0.1761	10879	X-RAY DIFFRACTION	94
3.91-4.21	0.176	568	0.1659	10801	X-RAY DIFFRACTION	94
4.21-4.63	0.1654	563	0.1567	10690	X-RAY DIFFRACTION	93
4.63-5.3	0.1822	526	0.1622	9997	X-RAY DIFFRACTION	87
5.3-6.67	0.2192	568	0.1934	10787	X-RAY DIFFRACTION	94
6.68-49	0.196	558	0.1871	10599	X-RAY DIFFRACTION	92

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	0.6841	-0.1021	0.2303	1.4093	0.0024	1.7543	0.0297	-0.0074	-0.0439	-0.2111	-0.0455	0.4955	-0.0241	-0.4259	0.0257	0.369	0.0171	-0.0642	0.3625	-0.0296	0.4464	-25.1347	14.17	9.4271
2	0.9049	0.9258	-0.0883	2.7736	0.4328	3.4632	-0.0437	0.0439	-0.0163	-0.2252	0.0237	-0.3441	0.0753	0.2393	0.0262	0.3833	0.0274	-0.0728	0.3003	-0.0152	0.3132	-9.7559	22.9126	4.7145
3	0.7509	0.6093	-0.1307	3.409	-0.9149	1.9622	-0.0035	-0.0265	0.1485	-0.0067	-0.077	-0.2911	-0.3278	0.1724	0.0388	0.4281	0.0279	-0.0482	0.3024	-0.0112	0.4161	-0.8856	44.7002	17.5908
4	1.5375	-0.3317	-0.6086	2.4805	0.5418	1.9278	-0.0646	-0.1598	-0.2447	0.3196	-0.0077	0.2716	0.3462	-0.1201	0.1296	0.4727	-0.0607	-0.0022	0.3266	0.0139	0.4158	0.6659	-27.8333	20.7313
5	1.038	-0.6576	-0.3024	1.2917	0.6591	0.9186	-0.0136	-0.17	0.0943	0.1808	0.0699	-0.259	-0.002	0.1877	-0.0557	0.3982	-0.021	-0.0514	0.2994	0.0176	0.288	15.582	-4.8561	24.9466
6	1.6004	-1.0548	-0.7816	2.1659	0.698	0.7552	0.2102	0.3404	-0.2202	-0.3995	-0.1541	-0.0747	-0.0076	0.0906	0.0031	0.3821	0.0195	-0.0495	0.3717	-0.0063	0.3741	22.1001	-16.2624	9.8097
7	1.5942	-0.57	-0.5004	2.3295	0.2325	1.5487	-0.0015	-0.0759	0.0236	-0.1315	0.184	-1.1576	0.0034	0.6216	-0.219	0.3724	0.0408	0.0214	0.5537	-0.0462	0.757	44.6	-17.3513	11.3128
8	3.0593	-0.1722	-0.6456	2.0347	0.4195	2.2174	-0.0279	0.0366	0.0603	-0.1334	0.0139	0.6815	-0.1047	-0.4988	0.0258	0.3782	0.0146	-0.0547	0.3688	0.0598	0.4695	35.1979	25.3311	-46.9695
9	0.6963	0.4202	-0.6278	1.8755	-0.2915	2.1947	0.0257	-0.1151	-0.0469	0.3948	-0.0363	0.3375	0.2211	-0.233	0.0212	0.3981	-0.0701	0.0667	0.382	0.0004	0.3758	40.6877	11.4029	-23.6716
10	0.5537	-0.9445	-0.9811	2.9925	1.7963	3.5677	-0.0531	-0.1909	0.0777	-0.0335	0.1748	-0.5412	-0.0851	0.5613	-0.1408	0.408	-0.0327	0.0044	0.4022	0.0592	0.4045	55.0125	11.5065	-32.8694
11	1.0396	-0.3885	0.3598	3.2943	-1.2637	3.5027	-0.0656	-0.0537	-0.3065	-0.0278	-0.0565	-0.229	0.7459	0.3295	0.0964	0.5276	0.0194	0.0397	0.3417	0.0143	0.446	59.2101	-11.7154	-42.3149
12	0.7492	0.433	0.1746	1.7662	0.5593	1.1026	-0.0603	0.1015	0.0988	-0.2655	0.0207	0.0902	-0.1618	-0.0156	0.0528	0.4302	-0.0405	-0.0052	0.3331	0.0187	0.2778	-52.9279	48.8709	-48.1288
13	2.1638	0.4674	0.8793	2.9427	0.6931	1.0431	0.1174	-0.4445	0.0221	0.5019	-0.0412	-0.0593	-0.0644	0.2087	-0.0548	0.4241	-0.0423	-0.0304	0.3613	-0.0105	0.2492	-42.9105	45.0357	-38.6956
14	1.0832	0.5082	0.3995	2.6786	0.2646	1.3673	-0.0133	0.0096	0.0068	0.2001	0.1882	-0.9586	-0.1256	0.6339	-0.1996	0.4405	-0.084	-0.0255	0.6241	-0.0921	0.6003	-18.4814	54.7548	-35.2812
15	1.1742	0.0261	-0.2571	3.551	-0.215	1.0889	-0.0536	0.3886	-0.0888	-0.4359	-0.1042	0.3821	0.1584	-0.112	0.0951	0.6116	-0.0024	-0.1731	0.4626	-0.1304	0.5678	-30.1889	-19.1822	-19.4709
16	1.3078	-0.3502	0.2355	1.2398	0.2792	0.5235	0.0146	0.2805	-0.0664	-0.3255	-0.0818	0.0987	-0.0227	-0.004	0.0415	0.5064	-0.0316	-0.057	0.3375	-0.0555	0.2975	-8.8298	-22.0991	-15.5995
17	2.5014	-1.0506	0.0718	1.634	-0.1143	1.8613	0.0331	0.4063	0.2856	-0.6899	-0.0741	-0.1194	-0.4826	0.1812	0.091	0.7754	-0.085	-0.0444	0.4415	0.0192	0.3647	-2.8352	-9.4412	-26.0924
18	2.182	-0.4901	0.2945	1.3316	-0.3293	1.3393	0.042	0.8838	0.5164	-0.9639	-0.1712	-0.096	-0.5012	0.0842	0.0992	1.3899	-0.0619	-0.0481	0.7861	0.133	0.5617	-4.638	0.9788	-43.639
19	1.9781	0.7824	-0.1889	2.4855	-0.1983	1.2307	0.1397	-0.3123	0.5964	0.7164	-0.1313	1.0076	-0.2518	-0.2415	-0.037	0.6302	-0.0015	0.2648	0.5022	-0.092	0.7828	35.0442	52.6485	-10.0801
20	1.3794	0.7947	-0.0644	2.1352	-0.1819	1.3246	0.2919	-0.7218	-0.2188	1.1524	-0.3232	0.0404	0.2992	0.0615	0.0519	1.1616	-0.0979	0.0879	0.7394	0.0198	0.4473	58.0039	42.4803	8.6964

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 329 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 330 through 506 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 507 through 797 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 20 through 184 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 185 through 405 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 406 through 591 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 592 through 797 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 21 through 184 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 185 through 405 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 406 through 566 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 567 through 797 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 23 through 372 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 373 through 540 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 541 through 796 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 20 through 83 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 84 through 329 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 330 through 451 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 452 through 796 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 19 through 184 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 185 through 796 )

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