PDB-6xs4: Crystal structure of glycyl radical enzyme ECL_02896 from Enterob...

ID or keywords:

Entry

Database: PDB / ID: 6xs4

Title

Crystal structure of glycyl radical enzyme ECL_02896 from Enterobacter cloacae subsp. cloacae

Components

Formate C-acetyltransferase

Keywords

LYASE / Glycyl radical enzyme / probable dehydratase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

transferase activity
Similarity search - Function

Biological species

Enterobacter cloacae subsp. cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.33 Å

Authors

Valleau, D. / Evdokimova, E. / Stogios, P.J. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of glycyl radical enzyme ECL_02896 from Enterobacter cloacae subsp. cloacae.
Authors: Valleau, D. / Evdokimova, E. / Stogios, P.J. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jul 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	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	6xs4.cif.gz	706.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6xs4.ent.gz	521 KB	Display	PDB format
PDBx/mmJSON format	6xs4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6xs4_validation.pdf.gz	453.3 KB	Display	wwPDB validaton report
Full document	6xs4_full_validation.pdf.gz	459.6 KB	Display
Data in XML	6xs4_validation.xml.gz	59.8 KB	Display
Data in CIF	6xs4_validation.cif.gz	85.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xs/6xs4 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xs4	HTTPS FTP

-
Related structure data

Related structure data	4mtjS S: Starting model for refinement
Similar structure data	5fau-2 1r9d-d 1r8w-d 5a0u-2 4mtj-d 5a0u-3 6nd3-1 5fau-1 6nd3-2 5a0u-5 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP96660

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Formate C-acetyltransferase

B: Formate C-acetyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology, Glycyl radical enyzmes of this variety have been generally characterized as homodimers.

Unit cell

Length a, b, c (Å)	283.101, 60.974, 118.951
Angle α, β, γ (deg.)	90.000, 107.653, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-1253- HOH

#1: Protein	Formate C-acetyltransferase Mass: 90302.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria) Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_02896 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CPF7
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.59 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 15% PEG3350, 0.1M Succinic Acid pH 7

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.33→39.7241 Å / Num. obs: 78987 / % possible obs: 95.37 % / Redundancy: 3.5 % / B_iso Wilson estimate: 39 Å² / R_pim(I) all: 0.045 / Net I/σ(I): 9.25
Reflection shell	Resolution: 2.34→2.38 Å / Num. unique obs: 3022 / CC_1/2: 0.943 / R_pim(I) all: 0.192

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4MTJ

4mtj

Resolution: 2.33→39.72 Å / SU ML: 0.2506 / Cross valid method: FREE R-VALUE / Phase error: 24.3435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2033	1996	2.53 %
R_work	0.1794	76823	-
obs	0.18	78819	95.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 53.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→39.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12682	0	23	722	13427

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0034	12960
X-RAY DIFFRACTION	f_angle_d	0.564	17557
X-RAY DIFFRACTION	f_chiral_restr	0.0423	1950
X-RAY DIFFRACTION	f_plane_restr	0.0031	2294
X-RAY DIFFRACTION	f_dihedral_angle_d	20.1887	4778

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 (%)
2.33-2.39	0.3276	99	0.2812	3811	X-RAY DIFFRACTION	67.33
2.39-2.46	0.3203	127	0.274	4879	X-RAY DIFFRACTION	85.28
2.46-2.53	0.2644	145	0.2594	5530	X-RAY DIFFRACTION	96.25
2.53-2.61	0.2477	146	0.2449	5620	X-RAY DIFFRACTION	98.85
2.61-2.7	0.272	148	0.2279	5674	X-RAY DIFFRACTION	98.81
2.7-2.81	0.2567	146	0.2213	5632	X-RAY DIFFRACTION	98.22
2.81-2.94	0.2613	144	0.2221	5550	X-RAY DIFFRACTION	96.71
2.94-3.1	0.2493	148	0.2096	5703	X-RAY DIFFRACTION	98.73
3.1-3.29	0.2435	148	0.2008	5683	X-RAY DIFFRACTION	99.45
3.29-3.54	0.1892	147	0.1857	5707	X-RAY DIFFRACTION	98.92
3.54-3.9	0.2008	145	0.1615	5607	X-RAY DIFFRACTION	97.01
3.9-4.46	0.146	150	0.1384	5764	X-RAY DIFFRACTION	99.51
4.46-5.62	0.1551	150	0.1443	5794	X-RAY DIFFRACTION	98.92
5.62-39.72	0.178	153	0.145	5869	X-RAY DIFFRACTION	98.16

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	5.74437150606	6.96605854754	-4.31254605367	8.58391695519	-4.50408821568	5.91951182581	1.62481657336	-2.33698850836	-1.09676665432	2.27903848962	-1.48240182184	-0.799134696213	-0.226124634364	0.0153259887141	-0.159653594316	1.06344263393	0.137180300384	-0.113665668152	0.994042615642	0.161162455452	0.573620047707	118.493734696	4.91902358765	53.3800259418
2	4.50682945932	0.199071551274	2.45395936434	4.88788985319	-2.83545503201	3.1638349006	-0.165249288971	-0.0656337529044	0.559176841089	0.367303047094	-0.222527414787	-0.692613907753	-1.5181314501	0.795437925985	0.402276522957	0.66442480128	-0.0777310923372	-0.0139269287017	0.439906097981	-0.0579573519875	0.575571340796	117.096573327	43.897264377	31.7649489884
3	3.13789757968	-1.35469240168	0.532270705554	1.74832456927	-1.77314860482	2.43828598357	0.128215728882	-0.0194425869018	0.0821499032302	0.0314976118951	-0.051005398265	0.0555404267479	-0.203344713068	0.0132184477348	-0.0742338670195	0.413735272182	-0.045190122025	0.0168937799686	0.307096601328	-0.0263702037924	0.2463944869	102.380995921	29.4953335328	25.4288569581
4	1.52452585086	-0.640158104465	0.542727188927	1.23192447865	-0.0804582021167	2.88896199616	0.0506550551683	0.0194665679432	-0.0897029529199	-0.0713198163049	0.0944297581773	-0.251076946521	0.503875060224	0.819141297997	-0.162410482363	0.564351558868	0.172353115811	0.033170167916	0.498393009631	-0.0536225614485	0.362052422718	121.234477133	14.8756661446	23.3222546147
5	3.18857775528	-2.68492792962	-3.88398463295	4.16790013669	2.71508077535	4.89049976398	-0.832879149928	-0.494665121564	-0.429320214123	1.19681389255	0.479739951442	-0.666328840179	1.98839962244	1.4600514207	0.334710380766	1.1124086149	0.418835098881	0.0204577171009	0.820236076747	0.14325635411	0.751676031255	125.41498127	-2.19402627538	38.5186345959
6	1.52894899289	-0.261273798082	0.394236729108	2.52413598462	-1.34400807	2.66698844654	-0.0277668584449	-0.187111076108	-0.232132766116	0.314116769937	0.127041025474	-0.0223019800395	0.656988600848	0.212995381784	-0.103833819418	0.695436113379	0.130463843526	0.00750294421284	0.49885095067	-0.0123711499833	0.332786152639	110.165503682	11.3400100493	41.9241123626
7	8.08718864474	1.81713001071	4.83840714209	2.39577140962	0.998997670109	5.35115834619	0.148508988719	-0.469547260805	-0.489382620077	0.0870577789991	0.108557742402	-0.0266409019432	0.891446504733	-0.319353042313	-0.29735516875	0.804970675424	-0.0169929989858	0.0457499881578	0.31584881075	0.0374220326018	0.344880361016	97.7970015152	7.77202032652	37.6487261208
8	1.35831073342	-0.156549162292	-0.308983468767	0.654403103615	-0.0375127999422	2.47923684042	-0.0661408584649	-0.267368401025	-0.0686001421124	0.14745926622	0.0985310890574	0.121801894006	0.137621885023	-0.257876397727	-0.0303434657505	0.516669206115	-0.0252440310602	0.0538479509187	0.328615194699	0.0234300013338	0.27387249193	87.3827610517	28.34099005	35.1345038014
9	6.00772274507	0.119256982697	-4.50480202722	1.47115255005	-3.08834859688	9.49701311162	-0.116634882374	-1.09982590347	0.40661082803	0.664892318981	0.435727221213	0.149984331925	-0.923005326318	-0.308559417572	-0.324028480352	0.943984793088	0.0286856931559	0.122202142063	1.01915612651	-0.0850218602392	0.36210356951	80.9307456813	38.105970139	62.0185188848
10	0.882094731654	-0.0420284982392	-0.0134388151544	0.604276462869	-0.0181761093283	1.86312837318	-0.021517267737	-0.492102165094	-0.0981916780159	0.208736990275	0.0657502785869	-0.0216986351867	0.366768901099	-0.11176245694	-0.0523364213112	0.683918246451	0.0528347437359	0.0497333439622	0.516058939935	0.0355087878016	0.335942413358	94.8057009489	20.8530009882	48.8238363047
11	1.38046774964	-0.295865498791	0.808608074022	1.83055828835	-0.876122507898	2.5394095014	-0.0315106485066	0.158836635666	0.279584059498	-0.135648836718	-0.0228402790701	-0.239542169138	-0.331394472493	0.265421957884	0.0601681159024	0.500977392671	-0.0654435996174	0.0735267647431	0.251432424804	0.0150931038373	0.406833471991	100.348894792	57.1425783808	-7.36427458812
12	8.02917182388	1.41859128632	3.22105854069	8.84280144415	-1.86096698085	2.17872307443	-0.550075454972	-0.00427721261447	1.03475957484	-0.127138735497	0.0431892754848	-0.568202929898	-1.94013450266	1.66199032979	0.473738256904	0.5294810511	-0.132757930401	-0.0285543523403	0.460603234014	0.0175053887833	0.671329021516	114.08923892	59.499270178	-3.5660888689
13	0.560950024943	-0.320815509015	0.110645854148	0.526280028701	-0.319381478284	1.30123616131	-0.0692130652678	-0.0802921187908	0.147430358789	0.0380431501236	0.0761070819179	-0.0414170728866	-0.062442258199	0.0894625771426	-0.00867530427118	0.367203387576	-0.0240470132694	0.0380806170477	0.230003207856	-0.00743367875102	0.261145815418	93.433651866	47.5098937311	-0.492771589655
14	1.11566494225	-0.174189964764	0.458957046829	0.798492810339	-0.0968524786804	1.66412057049	0.05722747331	0.154191173833	0.139708215057	-0.216583076207	-0.0383174164264	0.0367483752373	-0.134443297704	-0.00932028889112	-0.0206457236673	0.605226940251	0.0120751506055	0.0563094858305	0.278943920368	0.0522814323099	0.369276238966	84.5006832977	51.594423113	-19.7844671562
15	0.748652957085	-0.189333908619	0.218426242826	0.598571600591	0.343219320861	1.64955615213	0.0406069244524	0.290240587597	0.000935197135776	-0.113711211007	0.0112894483301	-0.0846000932923	0.237611407371	0.562406451298	-0.0424854175169	0.579750689604	0.0720482749658	0.0674624582708	0.452173279516	0.0116530364421	0.300249760576	104.427122024	27.7180308272	-19.8459681349
16	3.9453752863	1.05896231222	-2.11586735259	6.88124768109	-2.06049671076	1.47555704158	0.0689578289672	1.28024716068	-0.376420764654	-0.993618372375	0.0528224001448	-0.439300977749	-0.859159269842	1.01102408051	-0.121063846664	0.948216805634	0.114487480685	0.250733728283	1.17307938907	-0.0510537091877	0.429959751442	119.305446609	28.5701659608	-43.8309765724
17	1.84092583137	-0.114903452959	-0.494982828808	1.02429406868	0.397781762339	2.8008075547	0.0991266932096	0.516055758656	0.0270774093955	-0.267554675739	-0.0631917873131	-0.0156217473525	0.0852354368902	0.45467793114	-0.0309757632987	0.627657609409	0.0816886886959	0.0670965813271	0.499517586591	0.0144770987699	0.342111400931	102.795396995	29.6194459458	-27.7032027414
18	4.02412259515	1.84579090895	6.05436185339	1.03332633195	2.76443498633	9.10792971774	-0.641689679051	1.49359533765	1.00844631481	-1.74655114148	0.438923484976	0.313774264791	0.00135078780397	-1.01324395119	0.198026798857	1.29700772998	-0.0112102820895	0.0232482646704	1.23569147781	0.207018444224	0.623816986663	89.1299826952	48.7072546118	-46.5892564112
19	3.77721091205	2.22672196851	1.69533620773	4.2118698043	1.97984902295	3.8909146167	-0.430836095155	0.769251721913	0.47485022246	-0.734459325422	0.134129174893	-0.127863126145	-0.0847337302587	0.862184913475	0.297912460847	0.788626491251	0.0786211027219	0.078894779813	0.787379796136	0.188685365944	0.520487009962	97.3546347151	46.9529742715	-36.1602894169
20	9.73588488773	-2.84743426479	5.97352833401	2.0220105082	-2.57765864073	7.31173890637	0.101721186364	1.4119116261	-0.593195058623	0.25424862986	-0.118359928692	-0.225009921486	0.0708404440371	1.65180166891	-0.0180899692352	0.72266041246	0.07685622586	0.0716899130028	0.830265379364	0.014797089018	0.591531892415	105.813208144	50.5513216121	-28.7440254174

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 1:10
2	X-RAY DIFFRACTION	2	chain A and resid 104:128
3	X-RAY DIFFRACTION	3	chain A and resid 129:182
4	X-RAY DIFFRACTION	4	chain A and resid 183:298
5	X-RAY DIFFRACTION	5	chain A and resid 299:311
6	X-RAY DIFFRACTION	6	chain A and resid 312:404
7	X-RAY DIFFRACTION	7	chain A and resid 405:432
8	X-RAY DIFFRACTION	8	chain A and resid 433:597
9	X-RAY DIFFRACTION	9	chain A and resid 598:614
10	X-RAY DIFFRACTION	10	chain A and resid 615:810
11	X-RAY DIFFRACTION	11	chain B and resid 1:106
12	X-RAY DIFFRACTION	12	chain B and resid 107:123
13	X-RAY DIFFRACTION	13	chain B and resid 124:247
14	X-RAY DIFFRACTION	14	chain B and resid 248:411
15	X-RAY DIFFRACTION	15	chain B and resid 412:605
16	X-RAY DIFFRACTION	16	chain B and resid 606:615
17	X-RAY DIFFRACTION	17	chain B and resid 616:728
18	X-RAY DIFFRACTION	18	chain B and resid 729:739
19	X-RAY DIFFRACTION	19	chain B and resid 740:779
20	X-RAY DIFFRACTION	20	chain B and resid 780:802

-
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://pdbjlvh1.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