PDB-8sdc: Crystal structure of fluoroacetate dehalogenase Daro3835 apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 8sdc

Title

Crystal structure of fluoroacetate dehalogenase Daro3835 apoenzyme

Components

Alpha/beta hydrolase fold protein

Keywords

HYDROLASE / FLUOROACETATE / DEHALOGENASE / ALPHA/BETA HYDROLASE

Function / homology

alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase fold protein

Function and homology information

Biological species

Dechloromonas aromatica RCB (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.86 Å

Authors

Stogios, P.J. / Skarina, T. / Khusnutdinova, A. / Iakounine, A. / Savchenko, A.

Funding support

1items

Citation

Journal: Febs J. / Year: 2023
Title: Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases.
Authors: Khusnutdinova, A.N. / Batyrova, K.A. / Brown, G. / Fedorchuk, T. / Chai, Y.S. / Skarina, T. / Flick, R. / Petit, A.P. / Savchenko, A. / Stogios, P. / Yakunin, A.F.

History

Deposition	Apr 6, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8sdc.cif.gz	296.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8sdc.ent.gz	211.5 KB	Display	PDB format
PDBx/mmJSON format	8sdc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8sdc_validation.pdf.gz	420.3 KB	Display	wwPDB validaton report
Full document	8sdc_full_validation.pdf.gz	422.2 KB	Display
Data in XML	8sdc_validation.xml.gz	32.6 KB	Display
Data in CIF	8sdc_validation.cif.gz	52.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sd/8sdc ftp://data.pdbj.org/pub/pdb/validation_reports/sd/8sdc	HTTPS FTP

-
Related structure data

Related structure data	8sddC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (3) #165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Alpha/beta hydrolase fold protein

B: Alpha/beta hydrolase fold protein

hetero molecules

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

1

A: Alpha/beta hydrolase fold protein

hetero molecules

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

2

B: Alpha/beta hydrolase fold protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.172, 45.224, 75.185
Angle α, β, γ (deg.)	87.625, 75.565, 63.035
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Alpha/beta hydrolase fold protein Mass: 33122.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dechloromonas aromatica RCB (bacteria) / Gene: Daro_3835 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q479B8
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 979 / 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 Å³/Da / Density % sol: 38.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% (W/V) PEG3350, 0.2 M MGCL2, 0.1 M BIS-TRIS PH 5.5, CRYOPROTECTANT 2% (V/V) PEG 200 AND PARATONE

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.86→19.66 Å / Num. obs: 40571 / % possible obs: 94.3 % / Redundancy: 3.6 % / B_iso Wilson estimate: 13.81 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.049 / R_pim(I) all: 0.044 / Net I/σ(I): 17.7
Reflection shell	Resolution: 1.86→1.9 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.092 / Mean I/σ(I) obs: 9.4 / Num. unique obs: 2552 / CC_1/2: 0.987 / R_pim(I) all: 0.061 / % possible all: 90.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.15_3448	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.86→19.66 Å / SU ML: 0.1468 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 17.5825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1735	2127	5.24 %	RANDOM
R_work	0.1246	38440	-	-
obs	0.1271	40567	94.35 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 18.44 Å²

Refinement step

Cycle: LAST / Resolution: 1.86→19.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4642	0	2	979	5623

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	4798
X-RAY DIFFRACTION	f_angle_d	0.8973	6530
X-RAY DIFFRACTION	f_chiral_restr	0.0555	704
X-RAY DIFFRACTION	f_plane_restr	0.0059	863
X-RAY DIFFRACTION	f_dihedral_angle_d	20.1949	1754

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 (%)
1.86-1.9	0.1895	126	0.1354	2508	X-RAY DIFFRACTION	90.61
1.9-1.95	0.2187	110	0.1363	2497	X-RAY DIFFRACTION	91.51
1.95-2	0.1921	144	0.1321	2486	X-RAY DIFFRACTION	91.99
2-2.06	0.1876	145	0.1297	2526	X-RAY DIFFRACTION	91.6
2.06-2.13	0.1858	145	0.1268	2478	X-RAY DIFFRACTION	93.05
2.13-2.2	0.1826	146	0.119	2503	X-RAY DIFFRACTION	93.31
2.2-2.29	0.1758	155	0.1241	2529	X-RAY DIFFRACTION	93.62
2.29-2.4	0.1867	126	0.1261	2607	X-RAY DIFFRACTION	94.05
2.4-2.52	0.2048	137	0.1316	2584	X-RAY DIFFRACTION	94.81
2.52-2.68	0.1975	143	0.1386	2583	X-RAY DIFFRACTION	95.21
2.68-2.89	0.1705	153	0.1325	2563	X-RAY DIFFRACTION	95.63
2.89-3.18	0.1546	141	0.1274	2618	X-RAY DIFFRACTION	96.13
3.18-3.63	0.1601	141	0.1109	2632	X-RAY DIFFRACTION	97.03
3.63-4.57	0.1205	155	0.1029	2653	X-RAY DIFFRACTION	98.08
4.57-19.66	0.2012	160	0.1358	2673	X-RAY DIFFRACTION	98.71

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	7.37361496003	-2.08311227364	-2.16211416993	4.24234656286	-0.304894124541	4.42448812712	0.023356234598	0.36343839974	0.466991870521	-0.120688342466	-0.000737802153198	-0.197162261413	-0.17062893197	0.164922475175	-0.00944916110599	0.14237710484	-0.0190011777849	0.0105568552921	0.110836067964	0.00415930084089	0.0760829490886	-24.5360579489	22.2525386856	65.2815958145
2	1.33933868374	-0.0780505167048	-0.359948499062	1.27454318255	-0.151294348836	1.50368338823	-0.0369948649723	0.085683601208	-0.0593137512151	-0.049029623807	-0.0102667757053	0.0194310446004	0.0467946759871	0.0297375899692	0.0421280929208	0.0619139142617	-0.00472414818201	-0.00711286711119	0.0530808808548	-0.00549592681508	0.0657390837822	-30.0870134725	14.2317892461	74.3874350554
3	1.9979680009	0.0562220856879	-0.425160356019	1.43635102442	-0.00474416974311	1.60058629244	-0.0993578998151	-0.0327472107922	0.0194822646336	0.0600688824174	0.111220862	-0.106995018903	-0.0705214993604	0.105000906575	-0.00917109004553	0.0976306433941	-0.00105648770695	-0.000406284672473	0.0766842847256	-0.0214536680736	0.0543808183092	-32.8967746315	26.0454175726	92.308674523
4	1.64516902854	0.187022484313	-0.42441126866	2.84790792719	-0.301733554145	0.987138402542	-0.0275639346681	-0.097879677321	0.0480847072538	-0.0800680200075	-0.0686411900576	0.00630070680134	-0.00045905895915	0.034268177487	0.0657180696566	0.0812137407041	0.00981061419672	0.00850125016827	0.0737047795286	-0.00218507612129	0.0281999278665	-33.8555104478	22.4820891068	81.7189746022
5	1.64000881201	0.865516946257	-0.184572092603	2.07813055465	0.186877529288	1.7424150269	-0.0604394587376	-0.112067011032	-0.192416067807	0.167083157714	-0.00979805092507	-0.031230833507	0.186780915646	0.07555564224	0.0603617505275	0.105877735156	0.0376984308003	0.0137057890154	0.0834511579167	0.0195968681578	0.123763325967	-25.3485034537	6.77574862746	87.2351864469
6	8.62601942746	0.916438846359	-0.974021401271	9.24601464338	0.76215409467	6.87306683138	0.0390684299066	0.419919396877	-0.650079347506	-0.0563543352773	-0.107339189589	-0.179163507477	0.638050801359	0.208864622646	0.0871059975703	0.154504774968	0.0862334104218	0.000422828133747	0.128246660882	-0.0401000615259	0.210975953824	-18.0615631531	0.796287147761	76.4088642461
7	5.19366368446	-2.52089877673	-1.77134163438	4.21953497441	1.52465300822	1.30356656896	0.0323412705966	-0.312005847017	0.371777798949	0.0654137475033	0.00056616694081	0.000728349210393	-0.143047581668	-0.0378223735885	-0.0432717378513	0.167128301694	0.00929167156617	-0.0031189442896	0.12512448993	0.0034162811262	0.0955899960293	-46.8170025666	46.9118687472	123.892515503
8	1.0560611065	-0.104781889111	-0.298165685894	1.13266370333	0.35046273083	1.16282579321	-0.00722496987134	-0.0918552469458	0.037839246176	0.0437586668107	-0.0070862386092	-0.0221166185658	-0.00163067486695	-0.0189447611342	0.0153717959394	0.0499931615368	-0.0026450162145	-0.0142054513055	0.0766366007184	0.00625968259709	0.055321377628	-45.9334576609	33.5733677257	120.597007968
9	1.49021070146	-0.0674455665729	0.131184760652	2.41997552501	0.490332398572	1.51016389291	-0.0801574911233	0.0138392012037	0.0405404490119	-0.0790704620317	0.0632222466476	0.0147066282616	-0.0900394601425	-0.0934831100849	0.012282192565	0.0975574648398	0.00675667208726	0.00287988926736	0.083983319064	0.00214066928445	0.0487318299851	-41.874225644	30.9105988912	99.7441948688
10	1.76646845621	-0.600085207293	-0.260111136575	3.30282350339	-0.905401251307	1.64493104616	0.0598118950982	0.0957338005341	-0.00842007676792	0.085516863595	-0.0859482948926	-0.0484181484189	-0.122375056346	0.0451731386752	0.00543702993456	0.0723981967758	0.00127517238471	-0.0109870468583	0.0752470191201	-0.0361412237707	0.0175584917189	-40.5467213446	33.7665163332	110.632827462
11	1.47065915994	-0.956286224162	0.691471310338	2.609700379	-1.24543023166	2.2473611231	-0.0173686090959	0.0506613199108	-0.0944883597993	-0.179398216485	-0.0587158912702	0.0863896337043	0.218969485122	-0.14584593141	0.0605040301778	0.0815607221753	-0.0355763276085	0.00966382621366	0.135226386584	-0.00759248693427	0.105584996789	-56.390317214	24.0586851799	114.32705694
12	5.54795427106	0.528222028792	0.448056540666	4.09359181584	1.08023109401	4.85917092512	-0.118158841488	-0.794141363972	-0.396531896394	0.756423958933	-0.0783587423091	0.577057761077	0.273833573037	-0.451788352963	0.107824467454	0.162366681526	0.0207989324195	0.068450236233	0.282063144656	0.0268462696461	0.176187497333	-62.4121447849	27.9530355602	127.748498478

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:24)
2	X-RAY DIFFRACTION	2	(chain A and resid 25:141)
3	X-RAY DIFFRACTION	3	(chain A and resid 142:186)
4	X-RAY DIFFRACTION	4	(chain A and resid 187:232)
5	X-RAY DIFFRACTION	5	(chain A and resid 233:285)
6	X-RAY DIFFRACTION	6	(chain A and resid 286:296)
7	X-RAY DIFFRACTION	7	(chain B and resid 1:26)
8	X-RAY DIFFRACTION	8	(chain B and resid 27:141)
9	X-RAY DIFFRACTION	9	(chain B and resid 142:186)
10	X-RAY DIFFRACTION	10	(chain B and resid 187:232)
11	X-RAY DIFFRACTION	11	(chain B and resid 233:287)
12	X-RAY DIFFRACTION	12	(chain B and resid 288:297)

-
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