PDB-6wqp: GH5-4 broad specificity endoglucanase from Ruminococcus champanel...

ID or keywords:

Entry

Database: PDB / ID: 6wqp

Title

GH5-4 broad specificity endoglucanase from Ruminococcus champanellensis

Components

Endoglucanase

Keywords

HYDROLASE / Cellulase / xylanase / GH5 / endoglucanase

Function / homology

Function and homology information

cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function

Biological species

Ruminococcus champanellensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Bianchetti, C.M. / 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	Apr 29, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 17, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	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

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Download

PDBx/mmCIF format	6wqp.cif.gz	502.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6wqp.ent.gz	343.9 KB	Display	PDB format
PDBx/mmJSON format	6wqp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wqp_validation.pdf.gz	445.3 KB	Display	wwPDB validaton report
Full document	6wqp_full_validation.pdf.gz	446.3 KB	Display
Data in XML	6wqp_validation.xml.gz	32.1 KB	Display
Data in CIF	6wqp_validation.cif.gz	48.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wq/6wqp ftp://data.pdbj.org/pub/pdb/validation_reports/wq/6wqp	HTTPS FTP

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Related structure data

Related structure data	4im4SC 6mq4C 6pz7C 6q1iC 6ui3C 6wqvC 6wqyC 6xrkC 6xsoC 6xsuC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ui3-d 4e94-1 4w85-1 5xd0-1 5d9p-1 6q1i-1 4v1r-2 6xsu-1 1v5d-1 7cju-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Endoglucanase

B: Endoglucanase

hetero molecules

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

1

A: Endoglucanase

hetero molecules

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

2

B: Endoglucanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.980, 85.850, 87.200
Angle α, β, γ (deg.)	90.000, 96.538, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Endoglucanase Mass: 39822.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus champanellensis (bacteria) Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D4LAX7
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.33 Å³/Da / Density % sol: 47.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystals were grown from protein solution mixed with an equal volume of reservoir solution, 0.5% Jeffamine, 100 mM HEES pH 7.0, and 1.1 pM Sodium Malonate H 7.0 (Hampton Index HT screen: C9) ...Details: Crystals were grown from protein solution mixed with an equal volume of reservoir solution, 0.5% Jeffamine, 100 mM HEES pH 7.0, and 1.1 pM Sodium Malonate H 7.0 (Hampton Index HT screen: C9) in a SD2 format microplate set with a TTP Labtech Mosquito robot. Crystals were cryoprotected with 1.0% Jeffamine, 100 mM HEES pH 7.0, 1.1 M Sodium Malonate pH 7.0, and 20% ethylene glycol

Crystal

Density Matthews: 2.33 Å³/Da / Density % sol: 47.29 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals were grown from protein solution mixed with an equal volume of reservoir solution, 0.5% Jeffamine, 100 mM HEES pH 7.0, and 1.1 pM Sodium Malonate H 7.0 (Hampton Index HT screen: C9) ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2013
Radiation	Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.6→45.37 Å / Num. obs: 94298 / % possible obs: 97.62 % / Redundancy: 4.1 % / B_iso Wilson estimate: 17.19 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.1073 / R_pim(I) all: 0.06165 / R_rim(I) all: 0.1242 / Net I/σ(I): 8.31
Reflection shell	Resolution: 1.6→1.657 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.7174 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 9451 / CC_1/2: 0.681 / CC star: 0.9 / R_pim(I) all: 0.3954 / R_rim(I) all: 0.8206 / % possible all: 98.49

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IM4

4im4

Resolution: 1.6→45.37 Å / SU ML: 0.2051 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.6988

	R_factor	Num. reflection	% reflection
R_free	0.2422	2000	2.13 %
R_work	0.2029	-	-
obs	0.2038	94068	97.61 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.67 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→45.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5551	0	26	646	6223

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0055	5743
X-RAY DIFFRACTION	f_angle_d	0.7898	7844
X-RAY DIFFRACTION	f_chiral_restr	0.0483	865
X-RAY DIFFRACTION	f_plane_restr	0.0052	1023
X-RAY DIFFRACTION	f_dihedral_angle_d	12.276	2049

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 (%)
1.6-1.64	0.3188	100	0.2669	6615	X-RAY DIFFRACTION	98.45
1.64-1.68	0.3294	200	0.2459	6610	X-RAY DIFFRACTION	98.58
1.68-1.73	0.2507	100	0.2365	6680	X-RAY DIFFRACTION	98.86
1.73-1.79	0.3008	200	0.2344	6546	X-RAY DIFFRACTION	98.6
1.79-1.85	0.3071	100	0.2217	6690	X-RAY DIFFRACTION	98.85
1.85-1.93	0.279	200	0.2248	6551	X-RAY DIFFRACTION	98.8
1.93-2.02	0.2913	100	0.2068	6684	X-RAY DIFFRACTION	98.62
2.02-2.12	0.2725	181	0.1991	6560	X-RAY DIFFRACTION	98.14
2.12-2.26	0.2082	119	0.1931	6556	X-RAY DIFFRACTION	97.02
2.26-2.43	0.226	100	0.1821	6584	X-RAY DIFFRACTION	97.35
2.43-2.67	0.234	200	0.1919	6453	X-RAY DIFFRACTION	96.7
2.67-3.06	0.2138	100	0.1959	6486	X-RAY DIFFRACTION	95.23
3.06-3.86	0.2125	200	0.1934	6413	X-RAY DIFFRACTION	95.36
3.86-45.37	0.2328	100	0.2019	6640	X-RAY DIFFRACTION	96.15

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	0.0771830094641	0.0012086532603	-0.00531719515807	0.228344418497	-0.272035973379	0.174156580009	0.0769906495739	0.0276271553019	0.20588417113	0.279797695284	0.10173836034	-0.00533163028665	-0.0996276036846	-0.0235709476881	0.000738095823171	0.164373999274	0.00502576770177	0.0351260027852	0.105564306792	-0.0125393828539	0.199853843846	-5.0514230462	58.9512853473	-3.08584296454
2	0.341037096448	0.241874726833	0.0642674639564	0.520964954172	-0.150653477964	0.631282615835	-0.0427265541742	0.180778771693	-0.0432254193971	-0.0524910843476	-0.0106415235897	-0.0166833040182	0.0286510615807	0.108258076346	-5.06126463509E-7	0.115166793089	0.000662046438263	0.00412371067032	0.165394529814	0.0130431173349	0.127798351717	3.87890602266	48.0028358418	-22.7521980935
3	0.167365920825	-0.278105505679	0.0810784280457	0.652969763996	-0.118793030228	0.361825369755	-0.151129185428	0.198676143978	0.214758641878	0.00323788793935	0.0478005185719	-0.121850896547	-0.0752821687908	0.185419733673	-0.00221183300864	0.110724305931	-0.0157052737136	-0.0112913607764	0.148307076122	-0.00724756418627	0.097048644917	10.598577498	51.4336170985	-13.6351276421
4	0.313714968716	0.281174306894	0.116067806638	0.402955969852	-0.156498512812	0.956292457877	0.00862251828034	0.0201606185347	0.0223411092367	-0.0864017940952	-0.0168508356982	-0.0228529184535	-0.010047722424	0.0756586468769	-1.04975197511E-5	0.138870187947	-0.012408762842	0.0101036680257	0.0959533474634	0.00934669806757	0.100958109569	7.68967676	52.2419671713	-12.2638058774
5	0.122735740119	0.048520827152	-0.00474891901818	0.15311652279	0.0944115341325	0.0615992955449	0.0576050230102	0.118333216969	-0.0128565748757	0.0776874481303	-0.0627110440339	-0.0349297792438	0.000775262913508	0.177335240852	-2.72190605183E-5	0.110589117641	-0.0242899429508	0.0173287806249	0.190747867296	0.00953825533869	0.135427254451	17.7628844817	53.5111671344	-5.62875803919
6	0.875169958675	0.308554938621	0.326259010322	0.318504666285	-0.026416306144	0.538102305978	0.0448075005785	-0.0372531334139	0.0106828225402	0.0692321252396	-0.0772275342228	0.0327890955851	-0.0339989733738	0.0509041574639	-1.09586182239E-5	0.117573997976	-0.0129646301102	0.0145468267885	0.109362992857	-0.00369229466706	0.0917558181259	9.10998057108	48.9843105245	-0.820639111363
7	0.829936247258	-0.267986837251	0.0162044252111	0.129067437103	-0.0972433193063	1.02501407763	0.104841452969	-0.0499279696947	-0.0925002474169	0.0629695076452	0.0112643910629	0.0309040112015	0.105901667547	-0.0322317011889	0.00135887416109	0.13692399343	-0.0197867833264	0.00225387932669	0.121716185028	0.0125546634402	0.126015635238	-0.421404154958	39.5959504193	0.553068298608
8	0.0398611417451	0.225963874513	0.0948923114843	0.211030149173	-0.0945430117742	0.30476221472	0.0315647699107	-0.112890291605	-0.0299443134605	0.0928630243766	-0.00406622352784	0.0683044999873	0.174622124318	-0.108000188496	0.00106321309151	0.151267960072	-0.00507179423585	0.00999582972923	0.157131464216	-0.0172044563202	0.141348020324	-8.69759535508	38.0993349458	0.888812030405
9	0.708819142454	0.229964442409	0.385714769724	0.597975362977	-0.234462800919	0.442909366193	0.00476430762154	0.127140177915	-0.0320564515398	-0.0593290532059	0.0469311056913	0.102003724697	0.0329964543876	-0.12769285039	1.31833669777E-6	0.107313207056	-0.00522614780599	-0.0102386992053	0.150912445841	-0.00170319792375	0.126533680143	-12.3416099265	41.2770759279	-12.5816172615
10	0.018044283011	-0.128042479033	0.0179981978032	0.0682881053936	-0.137997618532	0.00114879658234	0.00305384715641	-0.0330120073307	0.13464039273	-0.160394162739	0.0185595975382	-0.0136804399866	-0.0414510948153	-0.0173885999192	0.0046096594357	0.231997663762	-0.0159308627255	-0.0125186013185	0.212653651065	0.0230748353532	0.208311186952	3.02911111114	65.1390792808	26.3979087541
11	0.36565302411	-0.298653903927	-0.0218916967808	0.240490648118	0.1334415635	0.804079877758	0.0257162998419	-0.126020333134	0.0676853819298	0.0399224407215	0.00274411895939	0.0398006560859	0.0140164565867	0.0023636867602	6.05425352162E-6	0.120281747611	-0.0150899015274	-0.00591784133675	0.142138841746	0.00605747697355	0.112510673074	-2.94172708937	51.3314908981	49.8676235642
12	0.134398656155	0.177928352937	-0.0139313267822	0.595173683059	0.24038293377	0.754306509235	0.00962164290237	-0.0602967012247	-0.00379699523106	0.0427685874703	-0.0434536963367	0.0948483788684	-0.0746586365662	-0.153463573397	-0.000157914707327	0.0996760516062	0.0187988520863	-0.0219043228209	0.0985030507159	0.0240073476168	0.0976504662895	-9.53102332607	54.1142152573	40.6388866453
13	0.822194880825	0.0968147987915	0.0169364607418	0.460771716327	0.298687096379	1.11471532619	0.0098256974958	0.0590877081927	-0.0329827309877	0.0266654284465	-0.0294295140277	0.0175212901686	-0.00837129822963	-0.0729527983213	-0.000197364526539	0.108802127855	0.00916152192787	-0.00362516714359	0.0941417944376	0.0128650216428	0.118274786552	-8.47329207065	51.5218605753	31.8424427839
14	0.793707896756	0.383445687266	0.143876561956	0.474862813647	0.330323864355	0.596958398578	0.115417949254	0.102524934672	-0.154020874559	-0.00578123304427	-0.0564729403313	-0.128242850135	0.170168866158	0.0780374024555	0.0019940514231	0.152993639281	-0.00832911058504	-0.0157200227264	0.113438529444	-0.00652305979411	0.129215457946	2.80950576742	41.7880278772	29.0015216713
15	0.420283816385	0.227506763765	0.0259848344164	0.160831511722	0.251500798554	0.453063515057	-0.00218142299251	0.107140318532	-0.226391296695	0.00595727314307	0.0256427828132	-0.142794405734	0.275875953604	0.267355253025	0.00605495430388	0.170644911036	0.0371416429692	0.0136129508872	0.179840612596	-0.00551111488147	0.184609853176	9.74793485174	39.303336603	27.3556940431
16	0.94093194359	-0.300875374484	0.0502568414256	0.630548260724	0.10395388806	0.299139024117	-0.0170374513444	-0.0991276664307	-0.197672277196	0.0304203111031	0.0270015424736	-0.0817691594844	0.173821895336	0.0966483448602	9.21836296264E-6	0.132689719303	0.00554468625399	0.00487347373073	0.171713744087	0.0256791731416	0.159120617751	13.3895574558	43.8410063334	40.4229678635

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 93 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 94 through 131 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 132 through 149 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 150 through 211 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 212 through 259 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 260 through 296 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 297 through 354 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 29 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 30 through 68 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 69 through 93 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 94 through 223 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 224 through 259 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 260 through 296 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 297 through 354 )

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-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