PDB-9np8: Crystal structure of the inactive conformation of a glycoside hyd...

ID or keywords:

Entry

Database: PDB / ID: 9np8

Title

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group I213 at 2.05 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 /

SAD / Resolution: 2 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 I213 at 2.05 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

-
Download

PDBx/mmCIF format	9np8.cif.gz	316.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9np8.ent.gz	256.5 KB	Display	PDB format
PDBx/mmJSON format	9np8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9np8_validation.pdf.gz	452.4 KB	Display	wwPDB validaton report
Full document	9np8_full_validation.pdf.gz	456.3 KB	Display
Data in XML	9np8_validation.xml.gz	34.5 KB	Display
Data in CIF	9np8_validation.cif.gz	46.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9np8 ftp://data.pdbj.org/pub/pdb/validation_reports/np/9np8	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycoside hydrolase family 2

hetero molecules

92.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycoside hydrolase family 2

hetero molecules

A: Glycoside hydrolase family 2

hetero molecules

A: 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)

Unit cell

Length a, b, c (Å)	191.802, 191.802, 191.802
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	199
Space group name H-M	I2₁3

#1: Protein	Glycoside hydrolase family 2 Mass: 91895.203 Da / Num. of mol.: 1 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.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61.55 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1 M ammonium phosphate dibasic, 0.1M sodium acetate, pH 4.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97913 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: 0.97913 Å / Relative weight: 1

Reflection

Resolution: 2→47.95 Å / Num. obs: 78790 / % possible obs: 99.7 % / Redundancy: 41.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.118 / R_rim(I) all: 0.12 / Net I/σ(I): 10.68

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2-2.12	3.525	24677	0.14	3.876	1
2.12-2.27	1.793	23329	0.361	1.979	1
2.27-2.45	0.899	21810	0.702	0.986	1
2.45-2.68	0.466	20011	0.891	0.514	1
2.68-3	0.207	18125	0.978	0.227	1
3-3.46	0.087	16005	0.996	0.095	1
3.46-4.23	0.043	13441	0.999	0.048	1
4.23-5.96	0.033	10396	0.999	0.037	1
5.96-47.95	0.029	5756	0.999	0.032	1

-
Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
XDS		data scaling
XDS		data reduction
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→45.21 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2125	3938	5 %
R_work	0.179	-	-
obs	0.1807	78773	99.99 %

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→45.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5931	0	16	324	6271

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6118
X-RAY DIFFRACTION	f_angle_d	0.617	8308
X-RAY DIFFRACTION	f_dihedral_angle_d	15.948	2234
X-RAY DIFFRACTION	f_chiral_restr	0.046	873
X-RAY DIFFRACTION	f_plane_restr	0.006	1082

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 (%)
2-2.02	0.3577	139	0.308	2670	X-RAY DIFFRACTION	100
2.02-2.05	0.297	140	0.2768	2650	X-RAY DIFFRACTION	100
2.05-2.08	0.305	138	0.2878	2621	X-RAY DIFFRACTION	100
2.08-2.11	0.2691	141	0.2596	2683	X-RAY DIFFRACTION	100
2.11-2.14	0.2671	141	0.2415	2685	X-RAY DIFFRACTION	100
2.14-2.17	0.2521	137	0.2417	2599	X-RAY DIFFRACTION	100
2.17-2.2	0.2512	140	0.2258	2654	X-RAY DIFFRACTION	100
2.2-2.24	0.2743	139	0.2286	2656	X-RAY DIFFRACTION	100
2.24-2.28	0.2933	141	0.2652	2674	X-RAY DIFFRACTION	100
2.28-2.32	0.2979	141	0.233	2680	X-RAY DIFFRACTION	100
2.32-2.36	0.2637	140	0.234	2653	X-RAY DIFFRACTION	100
2.36-2.41	0.2423	139	0.2224	2642	X-RAY DIFFRACTION	100
2.41-2.46	0.2585	139	0.2072	2650	X-RAY DIFFRACTION	100
2.46-2.52	0.2322	142	0.2052	2692	X-RAY DIFFRACTION	100
2.52-2.58	0.2362	139	0.2007	2631	X-RAY DIFFRACTION	100
2.58-2.65	0.2413	140	0.2091	2675	X-RAY DIFFRACTION	100
2.65-2.73	0.2032	142	0.2188	2686	X-RAY DIFFRACTION	100
2.73-2.82	0.2283	139	0.2103	2657	X-RAY DIFFRACTION	100
2.82-2.92	0.2476	141	0.2213	2670	X-RAY DIFFRACTION	100
2.92-3.04	0.3052	140	0.2401	2662	X-RAY DIFFRACTION	100
3.04-3.17	0.2556	141	0.2174	2668	X-RAY DIFFRACTION	100
3.17-3.34	0.2122	141	0.1887	2694	X-RAY DIFFRACTION	100
3.34-3.55	0.2193	141	0.18	2677	X-RAY DIFFRACTION	100
3.55-3.83	0.2035	142	0.1625	2698	X-RAY DIFFRACTION	100
3.83-4.21	0.1783	141	0.1423	2670	X-RAY DIFFRACTION	100
4.21-4.82	0.1624	143	0.1326	2722	X-RAY DIFFRACTION	100
4.82-6.07	0.1654	143	0.1481	2710	X-RAY DIFFRACTION	100
6.07-45.21	0.1976	148	0.1525	2806	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	0.7242	-0.2195	0.1908	1.2132	-0.4381	1.4787	0.0032	0.1423	-0.0386	-0.2225	0.0052	-0.0573	-0.0429	0.1733	0.0063	0.4654	-0.0332	0.0636	0.5166	-0.0386	0.3863	-30.8533	39.3	20.1225
2	0.8138	-0.4887	0.1925	1.6077	-0.1581	0.8615	0.0484	0.1046	-0.1711	-0.2111	0.0177	0.2557	0.0619	-0.0987	-0.0985	0.4442	-0.0276	-0.0469	0.4211	-0.0146	0.4079	-60.1985	33.624	22.1235
3	2.1915	0.7283	0.503	1.6	0.4648	1.2967	0.0609	-0.3876	-0.067	0.3187	0.1035	-0.2283	0.0098	0.0199	-0.0709	0.4738	0.0053	-0.001	0.4929	0.007	0.4317	-48.9235	37.244	36.863
4	0.9638	0.4177	-0.5837	1.814	-0.5691	1.5971	-0.0773	-0.0284	-0.4134	-0.2585	0.0633	-0.0969	0.5105	0.1869	-0.0233	0.685	0.0283	-0.0298	0.4142	-0.0468	0.6112	-47.0985	2.3437	31.3221

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 217 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 218 through 422 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 423 through 508 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 536 through 796 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi