PDB-6xrk: GH5-4 broad specificity endoglucanase from an uncultured bovine r...

ID or keywords:

Entry

Database: PDB / ID: 6xrk

Title

GH5-4 broad specificity endoglucanase from an uncultured bovine rumen ciliate

Components

Glycoside hydrolase type 1

Keywords

HYDROLASE / Cellulase / xylanase / GH5 / endoglucanase

Function / homology

Function and homology information

glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function

Biological species

uncultured bovine rumen ciliate (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.419 Å

Authors

Bingman, C.A. / Smith, R.W. / Glasgow, E.M. / Fox, B.G.

Funding support

United States, 2items

Organization	Grant number	Country
Department of Energy (DOE, United States)	DEFC0207ER64494	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	NIH 5 T32 GM008349 Biotechnology Training Program	United States

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis.
Authors: Glasgow, E.M. / Kemna, E.I. / Bingman, C.A. / Ing, N. / Deng, K. / Bianchetti, C.M. / Takasuka, T.E. / Northen, T.R. / Fox, B.G.

History

Deposition	Jul 13, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 28, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 4, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Feb 17, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6xrk.cif.gz	441.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6xrk.ent.gz	369 KB	Display	PDB format
PDBx/mmJSON format	6xrk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6xrk_validation.pdf.gz	456.8 KB	Display	wwPDB validaton report
Full document	6xrk_full_validation.pdf.gz	458.5 KB	Display
Data in XML	6xrk_validation.xml.gz	37.6 KB	Display
Data in CIF	6xrk_validation.cif.gz	59.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xr/6xrk ftp://data.pdbj.org/pub/pdb/validation_reports/xr/6xrk	HTTPS FTP

-
Related structure data

Related structure data	4im4C 6mq4C 6pz7C 6q1iC 6ui3C 6wqpC 6wqvC 6wqyC 6xsoC 6xsuC 2jepS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3m31-d 3b1p-d 5uvg-d 1rgu-2 1meh-d 5z1g-2 5vog-1 4r7j-d 2d1i-1 2y3y-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycoside hydrolase type 1

B: Glycoside hydrolase type 1

hetero molecules

86.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycoside hydrolase type 1

hetero molecules

defined by author
Evidence: gel filtration
43.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycoside hydrolase type 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.320, 84.990, 121.320
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

-
Protein , 1 types, 2 molecules AB

#1: Protein	Glycoside hydrolase type 1 Mass: 42883.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: uncultured ciliate from bovine rumen Source: (gene. exp.) uncultured bovine rumen ciliate (environmental samples) Plasmid: pVP67K Details (production host): Expression plasmid developed at the Center for Eukaryotic Structural Genomics Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3) / References: UniProt: G5DDB8, Hydrolases

#1: Protein

Glycoside hydrolase type 1

Mass: 42883.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: uncultured ciliate from bovine rumen
Source: (gene. exp.)

uncultured bovine rumen ciliate (environmental samples)
Plasmid: pVP67K
Details (production host): Expression plasmid developed at the Center for Eukaryotic Structural Genomics
Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3) / References: UniProt: G5DDB8, Hydrolases

-
Non-polymers , 5 types, 1037 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1029 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 nL 37 mg/mL protein, 50 mM sodium chloride, 10 mM MOPS, pH 7 + 200 nL reservoir solution (200 mM ammonium acetate, 100 mM Bis-Tris methane, pH 6.5, 25% PEG3350), MRC SD2 plate, ...Details: 200 nL 37 mg/mL protein, 50 mM sodium chloride, 10 mM MOPS, pH 7 + 200 nL reservoir solution (200 mM ammonium acetate, 100 mM Bis-Tris methane, pH 6.5, 25% PEG3350), MRC SD2 plate, cryoprotectant: reservoir solution + 35% PEG3350

Crystal

Density Matthews: 2.17 Å³/Da / Density % sol: 43.41 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 nL 37 mg/mL protein, 50 mM sodium chloride, 10 mM MOPS, pH 7 + 200 nL reservoir solution (200 mM ammonium acetate, 100 mM Bis-Tris methane, pH 6.5, 25% PEG3350), MRC SD2 plate, ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.774901 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2017
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.774901 Å / Relative weight: 1
Reflection	Resolution: 1.419→36.64 Å / Num. obs: 141292 / % possible obs: 100 % / Redundancy: 13.7 % / R_merge(I) obs: 0.07724 / Net I/σ(I): 18.36
Reflection shell	Resolution: 1.42→1.47 Å / Redundancy: 14.1 % / R_merge(I) obs: 1.415 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 13953 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2JEP

2jep

Resolution: 1.419→36.64 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.98

	R_factor	Num. reflection	% reflection
R_free	0.167	1997	1.41 %
R_work	0.145	-	-
obs	0.145	141196	100 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.419→36.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5723	0	40	1029	6792

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6044
X-RAY DIFFRACTION	f_angle_d	0.954	8231
X-RAY DIFFRACTION	f_dihedral_angle_d	13.074	2166
X-RAY DIFFRACTION	f_chiral_restr	0.078	889
X-RAY DIFFRACTION	f_plane_restr	0.006	1055

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 (%)
1.419-1.4554	0.3617	141	0.3495	9779	X-RAY DIFFRACTION	100
1.4554-1.4948	0.2854	140	0.2585	9850	X-RAY DIFFRACTION	100
1.4948-1.5388	0.208	141	0.2109	9860	X-RAY DIFFRACTION	100
1.5388-1.5884	0.2162	142	0.1829	9827	X-RAY DIFFRACTION	100
1.5884-1.6452	0.1873	142	0.1695	9895	X-RAY DIFFRACTION	100
1.6452-1.7111	0.1783	142	0.1599	9861	X-RAY DIFFRACTION	100
1.7111-1.789	0.1852	141	0.1552	9882	X-RAY DIFFRACTION	100
1.789-1.8833	0.18	142	0.1446	9893	X-RAY DIFFRACTION	100
1.8833-2.0013	0.2317	143	0.1441	9901	X-RAY DIFFRACTION	100
2.0013-2.1558	0.1643	142	0.1366	9946	X-RAY DIFFRACTION	100
2.1558-2.3727	0.1524	145	0.1309	9982	X-RAY DIFFRACTION	100
2.3727-2.7159	0.144	143	0.1299	10010	X-RAY DIFFRACTION	100
2.7159-3.4214	0.1358	143	0.1352	10104	X-RAY DIFFRACTION	100
3.4214-36.64	0.1598	150	0.1349	10409	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	1.3547	-0.1496	0.1452	1.1141	-0.0415	0.8182	0.0315	0.2398	0.0593	-0.1379	-0.0691	-0.0658	0.0414	0.1111	-0.0008	0.1604	0.0161	0.0141	0.2012	0.0234	0.1156	38.8434	56.9154	37.7355
2	1.1922	-0.4362	0.4423	0.7694	-0.109	0.6307	-0.1034	-0.0775	0.2601	0.1143	0.0112	-0.1911	-0.0628	0.1022	-0.0022	0.1549	-0.0229	-0.0209	0.1744	-0.0193	0.1994	48.4754	63.9688	56.9853
3	1.1721	-0.3124	0.2157	0.9429	-0.1393	0.9144	-0.039	-0.17	0.1904	0.1902	0.0141	0.0624	-0.1095	-0.0679	-0.0005	0.1646	0.006	0.0134	0.1728	-0.0226	0.1555	32.6552	64.4137	55.4517
4	0.7249	0.3176	0.1044	0.375	-0.2683	0.7367	0.0252	-0.0038	0.0143	0.038	0.0279	-0.1442	-0.0059	0.044	0	0.1119	0.0039	-0.0058	0.1168	0.0005	0.1394	73.2699	29.8323	38.1801
5	0.4789	0.2629	0.0724	1.3621	0.3542	0.846	0.0511	0.045	0.1079	-0.0313	-0.0079	-0.2754	-0.0587	0.0364	0.0004	0.1405	-0.0004	0.0131	0.1322	-0.01	0.1954	74.383	37.7779	37.9198
6	0.5264	0.229	0.4613	1.2702	0.1689	0.7735	0.0001	0.0308	0.1059	-0.1064	-0.0154	0.0009	-0.0638	-0.088	0	0.1653	0.0156	0.0013	0.1472	-0.0083	0.1284	62.0556	33.3706	32.2064
7	0.7834	0.1236	0.6276	0.9196	0.294	0.5444	0.0204	0.0412	-0.0244	-0.0934	-0.0559	0.0369	0.0436	-0.0748	-0	0.1682	0.0087	0.0025	0.1654	-0.0242	0.1328	60.3204	27.0687	31.179
8	0.7523	0.0955	0.1701	0.6969	-0.2013	0.2261	0.0408	-0.1631	-0.0125	0.2453	-0.1319	0.0673	0.125	-0.1795	0.0015	0.2149	-0.0415	0.003	0.2088	-0.0208	0.1424	58.0305	27.1635	50.5567
9	0.1637	0.012	-0.0047	0.1013	-0.039	0.015	-0.0049	-0.2577	-0.1772	0.4323	-0.1454	0.1229	0.3555	-0.312	-0.0164	0.4077	-0.0679	0.0061	0.2481	0.0425	0.2321	62.3137	14.6086	54.66
10	0.978	-0.254	-0.4053	0.647	-0.1217	0.4812	0.051	-0.1833	-0.1266	0.348	-0.0269	-0.187	0.2171	0.0307	0.0008	0.2603	-0.0082	-0.0561	0.1602	0.0064	0.1719	71.1026	21.4344	49.9406
11	0.2314	0.1237	-0.1152	0.0935	0.0532	0.547	0.0469	-0.0811	-0.094	0.3843	0.0713	-0.4488	0.2824	0.1607	-0.0149	0.2561	0.0339	-0.1411	0.1999	-0.0267	0.3096	82.5675	24.5328	52.467

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 200 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 201 THROUGH 273 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 274 THROUGH 357 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 1 THROUGH 34 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 35 THROUGH 119 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 120 THROUGH 161 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 162 THROUGH 200 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 201 THROUGH 247 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 248 THROUGH 273 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 274 THROUGH 328 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 329 THROUGH 357 )

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 1037 molecules

-
Details

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 1037 molecules

-Details

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 1037 molecules

-
Details

-
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